SERVICE MANUAL

VITRO S.A
Calle Luís Fuentes Bejarano. Edificio Nudo Norte (Local 3)
41020 Sevilla (SPAIN)
www.vitro.bio
T. +34 902 366 974
F. +34 902 366 977
e-mail: vitro@vitro.bio

MD-Stainer Service Manual V1._EN 1/173

 1 MD-STAINER INFORMATION....................................................................................... 11
2 MD-STAINER SOFTWARE PRODUCT LICENSE ............................................................... 12
3 AIM ........................................................................................................................... 13
4 RIGHTS AND WARRANTIES ......................................................................................... 14
4.1 Intellectual property ................................................................................................................. 14
4.2 Usage ........................................................................................................................................ 14
4.3 Documentation and general information ................................................................................. 14
5 INFORMATION AND SECURITY INSTRUCTIONS ............................................................ 15
6 TECHNICAL INFORMATION ......................................................................................... 16
6.1 Technical Data ........................................................................................................................... 16
6.2 Minimum requirements for a computer ................................................................................... 16
6.3 Serial number ............................................................................................................................ 16
6.4 Special tools .............................................................................................................................. 16
6.5 Installation Requirements ......................................................................................................... 16
6.5.1 Location ............................................................................................................... 16
6.5.2 Surface ................................................................................................................. 17
6.5.3 Electrical connections.......................................................................................... 17
6.5.4 Space Requirements............................................................................................ 17
6.5.5 USB connection ................................................................................................... 17
6.5.6 General Precautions ............................................................................................ 17
6.6 Content list ................................................................................................................................ 18
7 RECOMMENDED TOOLS .............................................................................................. 19
8 UNPACKAGING AND INSTALLATION ............................................................................ 20
8.1 Unpacking ................................................................................................................................. 20
8.2 Installation ................................................................................................................................ 20
8.3 Power and Connection .............................................................................................................. 21
8.4 Instrument Verification ............................................................................................................. 21
8.4.1 Verify Instrument Function ................................................................................. 21
8.4.1.2 Verify the Barcode Label Printing Function......................................................... 22
8.4.1.3 Verify Module Function....................................................................................... 23
8.4.1.4 Verify Barcode Reader Function.......................................................................... 23
8.4.1.5 Verify Probe Z1 Calibration ................................................................................. 23
8.4.1.8 Verify RFID Reader Function ............................................................................... 25
8.4.1.10 Exit (demo) ...................................................................................................... 26

MD-Stainer Service Manual V1._EN 2/173

 8.4.2 Create a Backup................................................................................................... 26
8.5 Verify Instrument Staining ........................................................................................................ 26
8.5.1 Verify the Extraction............................................................................................ 26
8.5.2 Verify the Deep Wash ......................................................................................... 26
8.5.3 Perform a Real Staining Run ................................................................................ 26
8.5.4 Verify the Staining Area Range............................................................................ 27
9 FEATURES BRIEF OVERVIEW ....................................................................................... 28
9.1 Overview of Main Components ................................................................................................ 28
9.2 Overview of Main Electronic Components ............................................................................... 29
9.3 Start-up the MD-Stainer Autostainer ........................................................................................ 30
9.3.1 Power ON the instrument ................................................................................... 30
9.3.2 Power ON the label printer ................................................................................. 30
9.3.3 Power ON and LOGIN to the computer............................................................... 31
9.3.4 LOGIN to the PCStainer UI ................................................................................... 31
9.4 Prepare Barcode Labels ............................................................................................................ 32
9.4.1 Open the Label Editor. ........................................................................................ 32
9.4.2 Prepare Labels. .................................................................................................... 32
9.4.3 Print Labels. ......................................................................................................... 33
9.5 Load and Unload Slides ............................................................................................................. 33
9.5.1 Affix Barcode Labels to Slides.............................................................................. 33
9.5.2 Load Slides. .......................................................................................................... 33
9.6 Auto Start Mode ....................................................................................................................... 34
9.6.1 Load Slides and Reagents .................................................................................... 34
9.6.2 Initiate Auto Start. ............................................................................................... 34
9.7 Manual Mode............................................................................................................................ 35
9.7.1 Load Slides ........................................................................................................... 35
9.7.2 Assign Protocols .................................................................................................. 35
9.7.3 Assign Reagents................................................................................................... 36
9.7.4 Verify Buffer and Waste Capacity ....................................................................... 37
9.7.5 Start the Staining Process.................................................................................... 37
9.8 End of the Staining Process ....................................................................................................... 38
9.8.1 Unload Slides ....................................................................................................... 38
9.8.2 Clean Up .............................................................................................................. 38

MD-Stainer Service Manual V1._EN 3/173

 9.8.3 Exit ....................................................................................................................... 38
9.9 Continuous Loading .................................................................................................................. 39
9.9.1 Stop the Current Staining Process ....................................................................... 39
9.9.2 Unload the Finished Slides .................................................................................. 39
9.9.3 Load the New Slides ............................................................................................ 40
9.9.4 Start the New Staining Process ........................................................................... 40
9.10 System Utilities ......................................................................................................................... 40
9.10.1 Baking Slides ........................................................................................................ 40
9.10.2 Check Heaters...................................................................................................... 40
9.10.3 Reagent Editor ..................................................................................................... 41
9.10.4 RFID Editor........................................................................................................... 42
9.10.5 Protocol Editor .................................................................................................... 42
9.10.6 Security ................................................................................................................ 43
9.10.7 Settings ................................................................................................................ 43
9.10.8 Network ............................................................................................................... 44
9.10.9 LIM ....................................................................................................................... 44
10 MAINTENANCE ....................................................................................................... 45
10.1 End-Customer Routine Maintenance ....................................................................................... 45
10.2 Technical Support Scheduled Routine Maintenance ................................................................ 46
10.2.1 Computer Maintenance ...................................................................................... 46
10.2.2 Cleaning and general inspection of the instrument ............................................ 46
10.2.3 Tubing Cleaning Procedure ................................................................................. 47
10.2.4 Components inspection ...................................................................................... 48
10.2.5 Calibration ........................................................................................................... 51
10.2.6 Final tests ............................................................................................................ 52
11 MODULE ................................................................................................................ 53
11.1 Overview of Module Components ............................................................................................ 53
11.2 Recommended Staining Area .................................................................................................... 54
11.2.1 Staining Area Range ............................................................................................ 54
11.2.2 MD_Stainer Tissue Slide Print Map ..................................................................... 54
11.3 Calibration: Module Agitation Heights ..................................................................................... 55
11.3.1 Using the Slides Interface .................................................................................... 55
11.3.2 Calibrating the “Home” Position ......................................................................... 57

MD-Stainer Service Manual V1._EN 4/173

 11.4 Troubleshooting: Module ......................................................................................................... 59
11.4.1 Symptom: Module lid is stuck. ............................................................................ 59
11.4.2 Symptom: Module stammer. .............................................................................. 60
11.4.3 Symptom: Module No Reply error. ..................................................................... 60
11.4.4 Symptom: Module goes to an unexpected agitation position. ........................... 60
11.4.5 Symptom: Chamber inserts unevenly. ................................................................ 61
11.4.6 Symptom: Slide does not insert into the module. .............................................. 61
11.4.7 Symptom: Module displays persistent Overheating and/or Low Temperature
warning during runtime. ..................................................................................................... 62
11.4.8 Symptom: Module fails the routine heater check. ............................................. 62
11.4.9 Symptom: Cannot connect to the Slides. ............................................................ 62
11.5 Maintenance/Repair: Module................................................................................................... 63
11.5.1 Chamber Cleaning and Replacement .................................................................. 63
11.5.2 Module Replacement .......................................................................................... 64
11.5.3 Module Repair ..................................................................................................... 66
12 ROBOT ................................................................................................................... 71
12.1 Overview of Robot Components ............................................................................................... 71
12.2 Extraction .................................................................................................................................. 72
12.2.1 Reagent Inject and Extract Test........................................................................... 73
12.2.2 Troubleshooting: Robot ...................................................................................... 75
12.2.3 Symptom: Probe is bent or off the original calibrated positions. ....................... 75
12.2.4 Symptom: Cannot connect to the Robot. ........................................................... 76
12.2.5 Symptom: Cannot initialize the Robot. ............................................................... 76
12.2.6 Symptom: Z2 and/or Z1 initialization error. ........................................................ 77
12.2.7 Symptom: X initialization error. .......................................................................... 78
12.2.8 Symptom: Y initialization error. .......................................................................... 78
12.2.9 Symptom: Z2 and/or Z1 do not respond. ............................................................ 79
12.2.10 Symptom: X or Y axes does not respond or responds intermittently. ............ 79
12.2.11 Symptom: LLD Sensor false negative detection. Reagent volume in vial is not
detected. 80
12.2.12 Symptom: LLD Sensor false positive detection. Reagent volume remaining in
vial is greater than expected. .............................................................................................. 80
12.3 Maintenance/Repair: Robot ..................................................................................................... 80
12.3.1 Bend Probe Z1 or Z2 ............................................................................................ 80

MD-Stainer Service Manual V1._EN 5/173

 12.3.2 Lubricate the Rail-Style ....................................................................................... 81
12.3.3 Clean the Optical Sensor ..................................................................................... 81
12.3.4 Replace the LLD Sensor Board............................................................................. 81
12.3.5 Replace the <?> Board or <?> Cable on the Robot. ............................................ 82
12.3.6 Verify the Dip Switch Settings on the Interconnect Board ................................. 83
12.3.7 Verify the Jumper Configuration on the XYZ Controller Board ........................... 83
13 RFID READER .......................................................................................................... 84
13.1 Overview of RFID Components ................................................................................................. 84
13.2 Troubleshooting: RFID Reader .................................................................................................. 84
13.2.1 Symptom: RFID Reader is not reading/writing all tags ....................................... 84
13.2.2 Symptom: RFID Reader is not reading/writing one or a few tags ....................... 85
13.2.3 Symptom: Data Read Error.................................................................................. 85
13.2.4 Symptom: Reagent Registration warning ........................................................... 85
13.2.5 Symptom: Cross-reading ..................................................................................... 85
13.2.6 Symptom: Cannot connect to the RFID Reader .................................................. 85
13.3 Maintenance/Repair: RFID Reader ........................................................................................... 86
13.4 Overview of 2D Barcode Reader Components ......................................................................... 89
13.5 Troubleshooting: Barcode Reader ............................................................................................ 89
13.5.1 Symptom: Barcode Reader is not reading any slide positions. ........................... 89
13.5.2 Symptom: Barcode Reader is not reading certain slide positions. ..................... 89
13.5.3 Symptom: Cannot connect to the Barcode Reader. ........................................... 90
13.6 Maintenance/Repair: Barcode Reader ..................................................................................... 90
14 HYDRAULICS SYSTEM (PUMPS, TUBING AND PROBES) ............................................. 92
14.1 Overview of the Tubing System Components ........................................................................... 92
14.2 Troubleshooting: Tubing ........................................................................................................... 93
14.2.1 Symptom: Liquid is leaking from the probe collet. ............................................. 93
14.2.2 Symptom: The probe is rusty. ............................................................................. 93
14.2.3 Symptom: A large number of bubbles appear in the tubing line after system
initialization. Liquid dispensation/aspiration is not reliable and is affecting staining quality.
93
14.3 Maintenance: Tubing ................................................................................................................ 93
14.3.1 Tubing Cleaning ................................................................................................... 93
14.3.2 Tubing Replacement............................................................................................ 94
14.4 Overview of Pump Components ............................................................................................... 98

MD-Stainer Service Manual V1._EN 6/173

 14.5 Troubleshooting: Pumps ........................................................................................................... 98
14.5.1 Symptom: Pump is producing abnormal noises or fails to initialize. .................. 98
14.5.2 Symptom: Pump produces a “clack” sound at every draw/dispense. ................ 98
14.5.3 Symptom: Pump plunger is stuck. ....................................................................... 99
14.5.4 Symptom: An extensive salt crust (may be discoloured) has built up around the
syringe and/or motor. ......................................................................................................... 99
14.5.5 Symptom: Z1 and/or Z2 pump does not respond. .............................................. 99
14.6 Maintenance: Pumps .............................................................................................................. 100
14.6.1 Pump Cleaning................................................................................................... 100
14.6.2 Pump Replacement ........................................................................................... 100
15 CALIBRATION INSTRUCTIONS ................................................................................ 103
15.1 Module Calibration ................................................................................................................. 103
15.1.1 Connect to the Slides......................................................................................... 103
15.1.2 Overview of Group Commands ......................................................................... 104
15.1.3 Overview of Module Commands....................................................................... 105
15.1.4 Calibrate the Home position ............................................................................. 106
15.1.5 Calibrate the Extract position............................................................................ 106
15.1.6 Calibrate the A7 position................................................................................... 106
15.1.7 Calibrate the Inject position. ............................................................................. 107
15.1.8 Calibrate the A4 position................................................................................... 107
15.1.9 Calibrate the A3 position................................................................................... 108
15.1.10 Calibrate the remaining agitation angles. ..................................................... 108
15.2 Robot Calibration .................................................................................................................... 108
15.2.1 Default Depths .................................................................................................. 109
15.2.2 References (Not implement / For future use)................................................... 110
15.2.3 Wash and Waste Station ................................................................................... 111
15.2.4 RFID Tag ............................................................................................................. 112
15.2.5 Barcode ............................................................................................................. 113
15.2.6 Reagent Vials ..................................................................................................... 114
15.2.7 Modules............................................................................................................. 115
15.2.8 Home ................................................................................................................. 117
15.2.9 Adjust Position Controls .................................................................................... 117
15.2.10 Apply Depth ................................................................................................... 118

MD-Stainer Service Manual V1._EN 7/173

 15.2.11 Safe Mode ..................................................................................................... 118
15.2.12 Show Coordinate (for advanced users only) ................................................. 119
16 COMPUTER........................................................................................................... 120
16.1 Setup a New Computer ........................................................................................................... 120
16.1.1 System Requirements ....................................................................................... 120
16.1.2 Setting Up a New Computer.............................................................................. 120
16.1.3 Copying the PCStainer Software to a New Computer ....................................... 120
16.1.4 Additional Windows Applications and Drivers .................................................. 121
16.1.5 PCStainer COM Port Assignment ...................................................................... 121
16.1.6 Setting the device SNR of the slide module Processor ..................................... 122
16.1.7 Setting the device SNR of the robot (xyzz system and pumps)......................... 124
16.1.8 Setting the RFID Reader COM Port# ................................................................. 126
16.1.9 Setting the 2D Barcode Reader COM Port# ...................................................... 128
16.2 Setup Network ........................................................................................................................ 128
16.2.1 System Requirements ....................................................................................... 128
16.2.2 Home Network Settings .................................................................................... 129
16.2.3 Shared Printer Settings...................................................................................... 131
16.2.4 Join the MD-Stainer Home Network ................................................................. 131
16.2.5 Configure the PCStainer Software to the MD-Stainer Home Network ............. 132
16.2.6 Configure the MD-Stainer Computer to use the Shared Printer....................... 133
16.2.7 Test the MD-Stainer Home Network for LIM/LIS Sharing and Label Printing ... 134
16.3 Setup LIS.................................................................................................................................. 135
16.3.1 Setup HL7 Server ............................................................................................... 135
16.3.2 Setup Computer ................................................................................................ 135

16.3.3 Open the HL7 connector application. .............................................. 136

16.3.4 Test the connection........................................................................................... 137
16.3.5 Access HL7 logs.................................................................................................. 137
16.4 Installing the Zebra Label Printer (currently compatible with models Zebra TLP3844-Z, GX430t)
138
16.4.1 Setting Up the Zebra Printer ............................................................................. 138

16.4.2 Installing the Zebra Setup Utilities and Printer Driver .......................... 138

MD-Stainer Service Manual V1._EN 8/173

 16.4.3 Configuring the Printer Settings ........................................................................ 138
16.4.4 Calibrating the Media ........................................................................................ 139
16.4.5 Printing a Test Label .......................................................................................... 139
16.5 Maintenance: Computer ......................................................................................................... 140
16.5.1 Clean-up Log Files .............................................................................................. 140
16.5.2 Backup Report Data........................................................................................... 140
16.5.3 Backup System Files .......................................................................................... 141
16.5.4 Perform General Computer Maintenance ........................................................ 141
17 SOFTWARE ........................................................................................................... 143
17.1 Software and Protocol Version ............................................................................................... 143
17.2 Software Installation Instruction ............................................................................................ 143
17.3 Troubleshooting: Software ..................................................................................................... 144
17.3.1 Symptom: Computer lost all calibration data and system settings. ................. 144
17.3.2 Symptom: System aborted or froze during the run. ......................................... 144
17.3.3 Symptom: System repeatedly aborts or freezes over several runs. ................. 145
17.3.4 Symptom: Yellow warning message displays on the slide map during the run.145
17.3.5 Symptom: Software displayed unhandled exception message or another
Windows error. ................................................................................................................. 145
17.3.6 Symptom: Autostainer server stopped working, not responsive, closed or frozen.
146
17.3.7 Symptom: Software is not responsive. ............................................................. 146
17.4 Staining Troubleshooting ........................................................................................................ 147
17.4.1 Weak Staining .................................................................................................... 147
17.4.2 Uneven Staining ................................................................................................ 148
17.4.3 Staining Background .......................................................................................... 149
17.4.4 No Staining ........................................................................................................ 150
17.4.5 Other Issues ....................................................................................................... 151
17.5 Instrument Troubleshooting ................................................................................................... 152
17.5.1 General Troubleshooting .................................................................................. 152
17.5.2 Symptom: Instrument does not power on. ....................................................... 152
17.5.3 Symptom: Cannot connect to the instrument. ................................................. 153
17.5.4 Symptom: Cannot connect to one or more devices. ........................................ 153
17.5.5 Symptom: Instrument running very slow or appears “frozen”. ........................ 154

MD-Stainer Service Manual V1._EN 9/173

 18 MISCELLANEOUS .................................................................................................. 155
18.1 Outer Housing Disassembly and Assembly ............................................................................. 155
18.2 Power Supply Replacement .................................................................................................... 156
18.3 Communications Board Replacement .................................................................................... 158
18.4 Other Electronic Boards Replacement .................................................................................... 160
19 GENERAL FAQS AND HOW-TOS ............................................................................. 164
19.1 FAQs ........................................................................................................................................ 164
19.1.1 Part I: Hardware ................................................................................................ 164
19.1.2 Software ............................................................................................................ 166
19.1.3 Protocols............................................................................................................ 167
19.1.4 Chambers Technology ....................................................................................... 167
19.1.5 Reagents and Waste.......................................................................................... 167
19.1.6 Cleaning and Maintenance................................................................................ 169
19.2 HOW-TOs ................................................................................................................................ 170
19.2.1 How to update the Reagents and Protocols in MD Stainer Software ............... 170

MD-Stainer Service Manual V1._EN 10/173

 1 MD-Stainer Information
MD-Stainer Model: SS1

Computer Configuration:

Laptop Computer or Tablet Computer with Mouse

Instrument Communications Interface: USB 2.0

USB Cable must be less than 3 meters (10 feet)

MD-Stainer Service Manual V1._EN 11/173

 2 MD-Stainer Software Product License

IMPORTANT: Please read the license carefully before using this Software. The right to use this
Software is granted only if the Customer agrees to the terms of this license

HOWEVER, USE OF THIS SOFTWARE INDICATES YOUR ACCEPTANCE OF THESE TERMS AND
CONDITIONS.

In return for the payment of the applicable one-time license fee included with the purchase price of
the MD-Stainer, Manufacturer grants the user a license to use one copy of the Software subject to the
following terms and conditions. No title or ownership of the Software is conferred with this license.

The Software may be used on one MD-Stainer. The Software may not be copied.

The Software may not be disassembled, decompiled, decrypted or reverse engineered.

Manufacturer reserves the right to terminate this license upon breach. In the event of termination at
Manufacturer’s election, all copies of the Software must be returned to Manufacturer.

No title or ownership of the Software is conferred with this license.

MD-Stainer Service Manual V1._EN 12/173

 3 AIM
This MD-Stainer manual is a referencing guide for the Technical Service Field Engineers when these
procedures are performed:

• Unpacking
• Hardware Installation
• Technical checkout
• Maintenance

MD-Stainer Service Manual V1._EN 13/173

 4 RIGHTS AND WARRANTIES
4.1 Intellectual property
All acts that violate the rights of intellectual property inherent to the product as a whole or any of its
components or parts are prohibited.

4.2 Usage
This device has been designed to be used in an in vitro diagnosis laboratory. We disclaim any liability,
in the event that the same or any component thereof is subject to misuse and / or use other than for
which it was designed. Users are the only responsible for the management, use, testing, processes
and outcomes that occur and are obtained with the instrument, or as an auxiliary device.

The manufacturer of the product or one of the components could not take responsibility for defects
when the product has been sold or misused in a market for which it was not designed for.

By means of CE marker, the manufacturer indicates that the device complies with the requirements
laid down in European Directives to be applied.

4.3 Documentation and general information

The manual supplied with the instrument is owned by Vitro, SA and is provided to customers and
authorized distributors for its use. Unless prior express written consent of Vitro SA authorization,
copying, dissemination and distribution- fully or partially- is forbidden, in any form and/or mean,
including all systems and electronic means, the text, images and illustrations contained in the manual.

The information contained in the manual (data, figures, drawings, technical details etc.) represent the
current state of scientific knowledge and latest technology as we understand it after conducting
thorough investigations in this field, and should not be considered as warranted as our products.

NOTE this depends on the commercial contract between the parties.

No liability, damages, financial loss or profit is accepted from or relevant to the statements contained
in the manual.

The manufacturer reserves the right to change the technical specifications and manufacturing
processes without notice. Only in this way it is possible to continuously improve technology and
manufacturing techniques used in our products.

MD-Stainer Service Manual V1._EN 14/173

 5 INFORMATION AND SECURITY INSTRUCTIONS
The following safety precautions and regulations must be observed when the instrument is used
particularly for medical diagnosis and in vitro. The failure to follow these instructions can lead to
reporting false negative results and the incorrect distribution of the samples.

I. All notes in the Service Manual should be read carefully, paying particular attention to the following
sections:

• Installation
• Disinfection procedures

II. The installation must follow these reasonable steps to ensure that the location where the
instrument is installed meets the environmental and electromagnetic specifications for the analyser.
Any significant movement of the equipment must be performed by qualified personnel.

III. The user should be informed and trained to perform daily maintenance and check to ensure the
correct operation of the instrument.

IV. Carefully, follow the instructions in the Service Manual for the operations to perform to turn on
and off the MD-Stainer.

V. All precautions and recommendations, normally used in the laboratory (good laboratory practice
standards), must be followed.

VI. If the laboratory does not have power sources protected, you may need an uninterruptible power
supply (UPS) to protect and nurture the team during a power outage.

VII. Using MD-Stainer do not ensure the absence of contamination by biological risk, so the instrument
should be handled as potentially infectious item and the usual precautions for these cases should also
be followed. Do not eat, drink or smoke while handling the device.

VIII. To reduce the risk of electric shock: Keep away from open circuits. The instrument must be
connected to a ground. The instrument must be equipped with a three-pole cable for connection to
230V or 115V.

MD-Stainer Service Manual V1._EN 15/173

 6 TECHNICAL INFORMATION
6.1 Technical Data
Environmental conditions Indoor use
Temperature range: 18-26ºC
Pollution degree: 1 or 2, in accordance with IEC 66
Manufacturing standards Meets applicable Safety and CE certified
Physical space requirement 153 x 61 x 54 cm
(W x D x H)
Power requirements Frequency: 50 to 60 Hz
Voltage: 110-240 V (Universal input)
Power consumption: 850W maximum
Software control Computer control via USB
Weight 50 kg
Slide Capacity 1 – 36 glass slides
Reagent Capacity 40 different reagents (15 mL/reagent vial)
Reagent Dispense Volumes 85-400 µL
Reagent Probe Volume 20 µL minimum, 4500 µL maximum
Capacity

6.2 Minimum requirements for a computer

Processor: Intel Core i5
Memory: 4 Gb
Hard Drive: 500 Gb
Operating System: Windows 7 (only 64 bits) or equivalent
USB ports free: 4 USB 2.0
Network Connection: Ethernet 10/100 Mbps – RJ45
Printer Zebra GX430t
UPS Minimum 1500 VA offline

6.3 Serial number

To get the serial number of manufacture of the product, see the label on the back side of the
instrument.

6.4 Special tools

Used for:
• Install modules and full calibration

Calibration Kit 13.5mm height gauge

6.5 Installation Requirements

6.5.1 Location
Place the system in an area where it is easy to operate and easy to connect to the instrument.

MD-Stainer Service Manual V1._EN 16/173

 6.5.2 Surface
The equipment must be installed over a flat and levelled surface

Prior to unpacking the Slide Stainer, ensure that the work area for the instrument is a solid, level
surface that can safely support the weight of the system (49.9 kg) for instrument plus computer.

6.5.3 Electrical connections

The Slide Stainer and computer need to be connected to a 120V/240 15A supply with grounding (3
prongs). Manufacturer recommends a dedicated power source for the Slide Stainer to prevent
interference from other instruments or equipment. An UPS (minimum 1500VA) is also recommended
if there are power spikes.

6.5.4 Space Requirements

Size Minimum dimensions for the Slide Stainer work area are 153 cm width x 61 cm depth x 54 cm
height clearance.

6.5.5 USB connection

The equipment must be installed close to the computer. The USB provided cable is 2 m long.

6.5.6 General Precautions

Make sure the slides are placed securely on the module – the slide should be pushed in against the
spring and the spring should push the slide back under the slide clips.

Place the reagent rack firmly in its seated position before starting a run on the instrument.

Remove caps from reagent vials before starting a run on the instrument.

Keep the door closed during operation. The robotic arm will move unexpectedly during operation -
stay clear. Do not impair the movement of the robotic arm in any way.

Contact your local MD-Stainer Representative prior to using reagents and solutions supplied by
other vendors on your Slide Stainer. Some solvents, acids, and other solutions may cause damage to
the internal components of the Slide Stainer and affect your instrument's performance and warranty.

Wear disposable gloves and protective lab wear when handling reagents. MD-Stainer Reagents are
harmful and irritating to the eyes, respiratory system and skin. It may cause lung and stomach damage
if ingested. MSDS (Material Safety Data Sheet) are available from your local MD-Stainer
Representative upon request.

Hazardous reagent wastes must be disposed of according to local, state and federal regulations.
Wear appropriate Personal Protective Equipment to prevent exposure.

MD-Stainer Service Manual V1._EN 17/173

 Do not multitask while the instrument is in operation. Multitasking is defined as running more than
one software application at a time (including CD players and screen savers). This may lock up the
instrument.

Disable Windows Automatic Update and other background programs while the instrument is in
operation.

Disable the Local/Wireless Internet Connection while the instrument is in operation.

Do not modify Windows Power options or install a screen saver. The computer may power off
unexpectedly while the instrument is still in operation or lock up the instrument.

Do not install third party software or hardware products. Installing third party products may lock up
the instrument and may void the warranty.

Do not make any hardware or software changes before consulting your local MD-Stainer Service
Representative.

Do not use a USB cable longer than 3 meters (10 feet).

Restart the computer if:

1. The USB is disconnected/reconnected. Always connect the USB to the designated USB port.

2. The power supply to the instrument is powered on/off or disconnected.

3. The computer is put into Sleep Mode or Hibernation Mode.

4. The user encounters an unexpected error.

Do not attempt to service the MD-Stainer Slide Stainer unless instructed to do so by an authorized
MD-Stainer Service Representative. Doing so will void the warranty.

Do not relocate the MD-Stainer Slide Stainer System within your facility before contacting your local
MD-Stainer Representative for vital information that may affect your warranty.

6.6 Content list

Please refer to the Service Bulletin SB-MDS-013-16 Packing List located at Vitro SharePoint site.

MD-Stainer Service Manual V1._EN 18/173

 7 RECOMMENDED TOOLS
Required Tools and Equipment
Imperial Allen Wrench Set
Phillips screwdrivers (small – medium – large)
Extender Tool for Flangeless Nut
Torx screwdrivers (T6 – T8 – T10)
Flat Head screwdrivers (small – medium – large)
Multimeter
Flashlight (headlamp recommended)
Cutting Plier
Pliers (small – medium)
Electrical Tape
Tweezers
ESD Wrist Tape
Infrared Thermal Detector
Lubri-Limp. Tuner and contact dry cleaner
WD40

MD-Stainer Service Manual V1._EN 19/173

 8 UNPACKAGING AND INSTALLATION
8.1 Unpacking
The MD-Stainer Slide Stainer is packaged in a wooden crate mounted on a pallet.

1. Unlatch all fasteners and remove the lid on top of the crate first.

2. Remove the computer, accessories box and label printer from the crate.

3. Remove the sides of the crate.

8.2 Installation

1. Requires 2 people. Each person should pick up one end of the Slide Stainer and carefully lift
it out of the crate. Carefully move the instrument to the operating area and place it on a solid,
level surface that can safely support the weight of the system.

2. Remove the 3 cable ties and 2 foam packaging blocks securing the robotic arm. With the
instrument still powered off, verify that the XYZZ axes can move freely before proceeding.

3. Cut the waste tubing to the proper length for the waste container. Connect the waste tubing
to the waste bottle(s). Ensure that there are no kinks or obstructions throughout the length
of tubing.

4. Level the instrument slide deck using a wrench to adjust the 4 feet up/down.

MD-Stainer Service Manual V1._EN 20/173

 a. Place a bubble level or other levelling tool on the deck plate.

b. Adjust the instrument so that the front side is slightly lower than the back side.

5. Install the computer and accessories following the instructions in the box.

8.3 Power and Connection

1. Plug the instrument and computer into a stable power source.

NOTE: A UPS (>1000W) is recommended for use with the instrument and computer.
Follow the instructions on the UPS, as some may require powering up for several hours to
charge the internal battery.

2. Two power switches are located on the instrument. Power on the switch on the back right-
side (ON/OFF power supply switch). Press and hold the blue switch located on the front or
side (stand-by switch).

3. Two designated USB ports are marked on the computer. Connect the instrument to the port
marked with the instrument serial number. Connect the label printer to the USB port marked
“Printer”.

4. Power on the computer and login. Default User Name: PathCom and Password: PathCom.

8.4 Instrument Verification

8.4.1 Verify Instrument Function

MD-Stainer Service Manual V1._EN 21/173

 NOTE: The MD-Stainer Software must be the last version and with the last protocol approved
by Manufacturer. You can locate it at Vitro SharePoint site.

8.4.1.1 Login and System Initialization

1. Double-click on the desktop shortcut link for the main user interface and
login.

2. Default user ID and password: “Distributor”

3. The system will take a few minutes to connect and initialize the instrument:

a. Robot XYZZ axes

b. Pumps 1 and 2

c. Modules 1-36

8.4.1.2 Verify the Barcode Label Printing Function

1. Click “Prepare Labels” to open the Slide Label Editor.

MD-Stainer Service Manual V1._EN 22/173

 2. Click “Add” and select several protocols.

3. Click “Save” and return to the Slide Label Editor.

4. Check the box, Select All, and click “Print” to print the selected barcode labels.

5. Affix the 2D labels on standard 1mm slides

8.4.1.3 Verify Module Function

1. Click “Load Unload Slides” to lift all 36 module lids to the Home position.

2. Insert labelled slides and click “Slide Lids Down” to lower all 36 module lids to the Down
position.

8.4.1.4 Verify Barcode Reader Function

1. Click “Scan Slides” to scan all 36 slides.

8.4.1.5 Verify Probe Z1 Calibration

1. Click System Utilities > SP1-Z1 Calibration to move Probe Z1 to module position #1.

MD-Stainer Service Manual V1._EN 23/173

 2. Verify the calibration: the tip of the Z1 probe should be centered and ~9/1000 inch above the
chamber chimney.

a. The X position is over the center of the chimney.

b. The Y position is between the center of the chimney and the back of the chimney wall.

c. The Z position is ~9/1000 inch (0.22 mm) above the chamber chimney.

3. Gently bend the probe to obtain the position as described.

4. Click “SP1-Z1 Calibration” again and re-check the calibration.

5. Click “Initialize System” after verifying the Z1 calibration.

8.4.1.6 Verify Probe Z2 Calibration

1. Click System Utilities > SP1-Z2 Calibration to move Probe Z2 to module position #1.

2. Verify the calibration using the method described above for Probe Z1.

3. Gently bend the probe if necessary and check the calibration again.

MD-Stainer Service Manual V1._EN 24/173

 4. Click “Initialize System” after verifying the Z2 calibration.

8.4.1.7 Verify the Door Lock

1. Click “System Utilities” to view the Tools tab.

2. Close the door of the instrument.

3. Click “Lock Door” and verify that the door locks securely.

4. Click “Unlock Door” and verify that the door unlocks smoothly.

8.4.1.8 Verify RFID Reader Function

1. Click “Scan Reagents” to open the Reagent Check screen.

2. Load the reagent rack with 40 RFID-tagged reagent vials.

3. Remove all caps from the reagent vials.

4. Click “Scan Reagents” to scan the reagent rack.

8.4.1.9 Schedule a Staining Run (demo)

1. After completing the reagent scan, check the boxes to verify the buffer and waste capacity.

MD-Stainer Service Manual V1._EN 25/173

 2. Click “Start Staining Process” to begin the run. The software will take a few minutes to
schedule the staining process.

8.4.1.10 Exit (demo)

1. The software will display a message “Run Successfully Ended” when the staining process is
complete.

2. Click “OK” to close the message box.

3. Click “Load Unload Slides” to remove the slides.

4. Click “Exit” to close the main user interface. The software will take a few minutes to close all
related applications and lift the 36 module lids up to the Extract position.

5. Power off the instrument. Press and hold the blue switch located on the front right-side.
Switch off the power supply switch on the back right-side to fully power off the instrument.

8.4.2 Create a Backup.

1. After verifying instrument functionality, create a backup of the PathCom folder on both an
external drive and the local disk C:/ for easy recovery in case of a system failure.

8.5 Verify Instrument Staining

8.5.1 Verify the Extraction

Perform an Extracting Test. Refer to 12.2. Extraction

8.5.2 Verify the Deep Wash

Perform a Wash Test. Refer to 15.2. Robot Calibration

8.5.3 Perform a Real Staining Run

The recommended tissue placement area for instrument verification is defined below. The placement
of tissue B is essential to verifying 1) the overall staining area and 2) the agitation heights.

MD-Stainer Service Manual V1._EN 26/173

 1. Run 36 slides on the instrument with an Ab to verify staining consistency.

2. MD-Stainer Validation Kit

3. Suggested Abs: TBD

8.5.4 Verify the Staining Area Range

Refer to 11.2.1. Staining Area Range for more details.

MD-Stainer Service Manual V1._EN 27/173

 9 Features Brief Overview
9.1 Overview of Main Components
Quantit
Part No. Description Function Image
y

X, Y, Z1, Z2 axes
PAT-PC701 XYZZ Robot 1 N/A
mechanism

PAT-PC800 Module 36 Stains slide

Operates and runs

PAT-PC330 Computer 1 PCStainer SW, requires 1
computer per instrument

RFID Reader System with RFID Reader system for

PAT-PC802 1
Antenna reading/writing RFID tags

Barcode Reader system

2D Barcode Reader System
PAT-PC801 1 for reading 2D barcode
with Cables
labels

PAT-PC704 Label Printer 1 Prints 2D barcode labels

Z1 dispenses reagent, Z2
PAT-PC703 Pump, 5mL 2
extracts waste

PAT-PC805 Tubing Kit with Probe 1 Z1 and Z2 fluid line

PAT-PC314 Fan 2 Passive cooling system

MD-Stainer Service Manual V1._EN 28/173

 PAT-PC318 Linear Interlock (solenoid) 1 Safety interlock for door

9.2 Overview of Main Electronic Components

Part Quantit
Description Function Image
No. y

Central communications;
PAT-
Communications Board 1 4 COM Ports Robot,
PC304
Slide, RFID, Barcode

PAT-
Backplane PCB 1 Connects to 36 modules
PC301

Connects
PAT-
Internet Cable 1 Communications to
PC312
Backplane

Converts power from

PAT- power supply to
12-24V Power Converter 1
PC303 Interconnect and
Communications

Power cable from RFID

PAT- Adapter B to
24V Power Converter Cable 1
PC310 Interconnect and
Communications

PAT- Adapter for RFID Module

RFID Adapter A 1
PC305 and RFID Ribbon Cable

Adapter for Fans, RFID

PAT-
RFID Adapter B 1 Ribbon Cable and RFID
PC306
Communications Cable

PAT- Connects RFID Reader

RFID Ribbon Cable 1
PC316 Adapter A to Adapter B

MD-Stainer Service Manual V1._EN 29/173

 Connects
PAT-
RFID Communication Cable 1 Communications to RFID
PC308
Adapter B

Connects
PAT-
Robot Communication Cable 1 Communications to
PC309
Interconnect

Connects
PAT- Communications to linear
Interlock Cable 1
PC311 solenoid and interlock
switch

PAT-
Power Supply 1 Main power supply
PC323

PAT- Switch to turn

Power Switch Cable 1
PC307 instrument on/off

9.3 Start-up the MD-Stainer Autostainer

9.3.1 Power ON the instrument

1. Locate the two power switches on the instrument and turn them on.

a. Back right-side switch (power supply on/off switch)

b. Front right-side or side switch (stand-by switch, press and hold)

NOTE: It is recommended to completely power off the instrument during extended periods of
disuse i.e.: weekends and holidays.

9.3.2 Power ON the label printer

1. Verify that the printer is connected to the computer in the designated port.

MD-Stainer Service Manual V1._EN 30/173

 9.3.3 Power ON and LOGIN to the computer

NOTE: To avoid connection issues, ensure that the instrument has powered on before starting
up the computer.

1. Login to the computer:

a. Default User Name: PathCom

b. Default Password: PathCom

2. Wait a few minutes for Windows to complete start up before launching the PCStainer
software.

9.3.4 LOGIN to the PCStainer UI

1. Verify that the instrument is connected to the computer in the designated port.

2. Open the PCStainer application on the desktop and login with the Distributor account:

a. Default User ID: “Distributor” (case sensitive)

b. Default Password: “Distributor” (case sensitive)

3. Wait a few minutes for the system to initialize the robot, pumps and slides.

MD-Stainer Service Manual V1._EN 31/173

 NOTE: The User ID may be generated under 3 different access levels that limit features to
certain users (see System Utilities > Security): Distributor (level 3), Supervisor (level 2), and Technician
(level 1)

9.4 Prepare Barcode Labels

9.4.1 Open the Label Editor.

1. Click to open the Slide Label Editor.

2. For systems connected to a LIM/LIS, a list of 2D barcode labels will be automatically

downloaded from the LIM/LIS and displayed on the above UI. The PCStainer software will
automatically synchronize and update the system status to the LIM/LIS database after the
label is selected to print, scanned for staining etc.

9.4.2 Prepare Labels.

1. Click “Add” to open the Barcode Editor and manually prepare 2D barcode labels.

2. Input the Patient ID, Case Number, Date etc. in the designated fields.

NOTE: Each label will be valid for 30 days after the date assigned on the label.

3. Input the Hospital or Distributor Name; Description or Pathologist.

NOTE: Block ID, Specimen Type, Doctor will not be printed on the label.

4. Select the protocol(s) from the list of Available Protocols, and click "Add". Click "Save" to add
the labels to the list of 2D barcode labels.

MD-Stainer Service Manual V1._EN 32/173

 9.4.3 Print Labels.
1. Select the check boxes or click “Select All” to select labels for printing.

2. Click “Print” to print the selected labels.

NOTE: All printed labels are automatically archived and can be viewed under Printed
Slides in the dropdown list.

9.5 Load and Unload Slides

9.5.1 Affix Barcode Labels to Slides.

1. Affix the printed barcode labels to the prepared slides.

9.5.2 Load Slides.

1. Click to move the lids up, and insert the slides.

2. Click to move the lids to the Down position.

MD-Stainer Service Manual V1._EN 33/173

 9.6 Auto Start Mode

9.6.1 Load Slides and Reagents

1. Prepare labels.

2. Load the labelled slides.

3. Load RFID-tagged reagents vials.

a. Place reagents in the reagent rack.

b. Remove all caps from reagent vials.

c. Place the reagent rack on the deck plate. Verify that it is securely seated.

4. Check that there is a sufficient volume of wash buffer in the buffer bottle and sufficient waste
capacity in the waste container.

9.6.2 Initiate Auto Start.

1. Click to begin staining.

2. The system will prompt the user to enter the number of labelled slides loaded onto the
system.

3. The system will automatically Scan Slides and Scan Reagents and then proceed to generate a
schedule and execute the staining process. The auto mode will be paused or cancelled if:

a. The number of expected slides input in the prompt does not match the number of
slides scanned.

b. Any required reagent for protocol is not satisfied in terms of:

i. Missing the reagent

ii. Reagent is expired.

MD-Stainer Service Manual V1._EN 34/173

 iii. The number of tests is not sufficient.

c. The number of protocols exceeds the limitations of the system.

9.7 Manual Mode

9.7.1 Load Slides

1. Prepare the labels.

2. Load the slides.

9.7.2 Assign Protocols

1. (Option 1) Manually Scan Slides

a. Click to scan all 36 slides.

b. Alternatively, select a group of slides and click to scan individual slides.

2. (Option 2) Manually Assign Protocols

a. The user may manually add new slides without labels and without scanning the slides.

b. Select a group of slides and click and select the protocol from the dropdown
list.

MD-Stainer Service Manual V1._EN 35/173

 9.7.3 Assign Reagents
1. (Option 1) Scan Reagents

a. Load RFID-tagged reagents vials. Place the reagents in the reagent rack. Remove all
caps from reagent vials.

b. Place the reagent rack securely in the designated area.

c. Check that there is a sufficient volume of wash buffer in the buffer bottle and
sufficient waste capacity in the waste container.

d. Click to open the Reagent Check screen.

e. The list of required reagents will be displayed on the right. The user may refer to this
list to fill in the reagents on the rack.

f. Click “Scan reagents” to start scanning the reagent rack.

g. The RFID reader will continue scanning the rack until all reagents on the list have been
found, or all 40 reagent rack positions have been scanned.

h. The staining process cannot proceed until all required reagents are scanned or
manually assigned.

2. (Option 2) Manually Assign Reagents

a. In the case of RFID reader error, or missing and insufficient reagents etc., the user may
manually assign reagents.

MD-Stainer Service Manual V1._EN 36/173

 b. Select the missing/insufficient reagent from the list on the right, then click on an
available reagent rack position on the left. Check that the reagent is placed in the
selected reagent rack position.

c. If an expired reagent has been scanned, the user must replace the reagent and re-
scan the reagent rack.

9.7.4 Verify Buffer and Waste Capacity

1. Verify the buffer and waste volumes before starting the staining process. The system cannot
proceed until the two boxes (see below) are checked. The volumes displayed are the
maximum volume the system can consume, up to a volume limit of 2 Litres.

9.7.5 Start the Staining Process

1. (Option 1) Start

a. Click to immediately begin the staining process. The system will initialize and
calculate the schedule. A clock will be displayed at the top of the screen, counting
down the time left to finish the process.

2. (Option 2) Delay Start

a. Click to begin the staining process at a later time.

b. Enter the expected finish time, and the system will calculate the required start time.

c. If the expected finish time does not allot sufficient time for the run to complete, the
user may choose to start staining immediately or reset the expected finish time.

MD-Stainer Service Manual V1._EN 37/173

 d. A clock will be displayed, counting down time left to start the process. The user may
cancel the delay start at any time while the clock is counting down.

e. Click to cancel and return to the main screen. All scanned data/manual
assignments will be lost.

9.8 End of the Staining Process

9.8.1 Unload Slides

After the staining process has completed, the system will display a pop-up message “Run Successfully
Ended.”

1. Click “OK” to close the pop-up message.

2. Click to move the lids up, and remove the stained slides.

9.8.2 Clean Up
1. Wipe the chamber surfaces with an alcohol pad after each staining process to remove
DAB/residues that have accumulated on the chamber surfaces.

2. Clean and dry the modules heaters and deck plate etc. using a soft paper tissue/towel.

9.8.3 Exit

1. Click to exit the PCStainer GUI. The system will shut down all applications and lift the
lids to the extract position. Please wait for the system to complete all processes before
shutting down or proceeding to the next staining run.

2. Login again to proceed with the next staining run.

MD-Stainer Service Manual V1._EN 38/173

 9.9 Continuous Loading
The user may also choose to load additional slides onto the system before the end of the current
staining process.

NOTE: Using this feature may significantly increase the total run time for all remaining slides
in the run.

9.9.1 Stop the Current Staining Process

1. Click to stop the progress of each slide once it has reached a safe point in the staining
protocol.

NOTE: The system will not stop until all slides are stopped, therefore, the wait time will
vary depending on the combination and type of active slides in the current staining process.

9.9.2 Unload the Finished Slides

After the system has stopped the progress of all slides, system will display a popup message “Run
Successfully Stopped”.

1. Click “OK” to close the pop-up message.

2. Remove all finished slides (lids will automatically lift up).

MD-Stainer Service Manual V1._EN 39/173

 9.9.3 Load the New Slides
1. Load the new slides in the available module positions that have been cleared by the finished
slides.

2. Prepare new labels and scan the new slides, or manually assign protocols as needed.

9.9.4 Start the New Staining Process

1. Load any additional reagents that may be required and re-scan the reagent rack.

2. Re-start the staining process. The system will reschedule the run to incorporate the new slides.
The new slides will take priority, and will run separately until they catch up with the Stopped
slides. The remaining common steps in the Set may be grouped between the new slides and
the Stopped slides.

9.10 System Utilities

Click to access additional user features.

9.10.1 Baking Slides

1. Click Tools > Baking Slides and select the module positions from the display.

2. Click Start to begin baking. The baking time is displayed on the left.

3. Click Settings > Baking Slides Settings to set the baking time and temperature.

9.10.2 Check Heaters

The system will display a “Low Temperature” or “High Temperature” warning if an abnormal
temperature was recorded during the staining process.

1. Click Tools > Check Heaters to verify the function of all heaters.

MD-Stainer Service Manual V1._EN 40/173

 NOTE: The heater check will require 10-15 minutes to verify all 36 slides. After the check, all
malfunctioning heaters will be marked in RED and locked out. The module cannot be used in staining
until the heater is replaced and a new heater check is performed.

The user is advised to perform a heater check regularly to ensure that all heaters are functioning
properly.

9.10.3 Reagent Editor

1. Click Editors > Reagent Editor to manage reagents.

2. For general reagents: select the Reagent Type, enter the new reagent name and click “Save”
to create a new reagent. Duplicate reagent names are not allowed.

3. For antibodies (or probes if available option): select the Reagent Type, enter the antibody
name AND the new protocol name and click “Save” to create a new antibody and its
corresponding protocol. The system will automatically generate a protocol using the template
of that Reagent Type. If the same antibody can be run using multiple detection systems, it may
be added once under each applicable Reagent Type. Duplicate protocol names are not
allowed.

4. For hazardous reagents: select the Reagent Type, enter the new reagent name and check the
box, “Yes”, under Hazardous before clicking “Save”. The system will classify the reagent as
“Hazardous” and will dispense all of the hazardous waste in the Hazardous Wash Station.

NOTE: The user must delete and re-create an existing reagent in order to change its
Hazardous status.

MD-Stainer Service Manual V1._EN 41/173

 9.10.4 RFID Editor
1. Click Editors > RFID Editor to read/write RFID tags.

2. The RFID Reader antenna will automatically move to the lower right side of the reagent rack.

3. Position the tag directly beneath the antenna coil.

4. Select the Reagent Type and Reagent Name. Enter the tag information in the required fields.

5. Click “Write Tag” to program the data into the tag.

6. Click “Read Tag” to read the data back from the tag.

NOTE: The Stand-Alone RFID Reader is recommended to all distributors. Refer to the MD-
Stainer Stand Alone RFID Reader Operating Manual.

9.10.5 Protocol Editor

1. Click Editors > Protocol Editor to view and edit protocols.

MD-Stainer Service Manual V1._EN 42/173

 2. It is recommended to use the manufacture default customizations. If needed, modify each
protocol using the options listed below if necessary:

a. IHC Primary Ab incubation Time and Temperature.

b. Target Retrieval Option and Temperature.

c. Dewax Solution 2 Option.

3. Click “Save” to save the changes to the protocol.

4. Click “Refresh Protocols with Customizations” to revert the protocol to the saved
customizations.

5. Click “Go Back to Manufacturer Default” to revert the protocol to the manufacturer’s default
customizations.

The editor provides the flexibility to modify the protocols, but these modifications may impact the
total run time. Further details are available in Protocols Fine Tuning Guideline.

9.10.6 Security
1. Click Security to change the login password(s) and manage user accounts.

9.10.7 Settings
1. Click Settings to manage general system settings.

MD-Stainer Service Manual V1._EN 43/173

 2. Click “2D Barcode Format” to adjust the label printing format.

3. Click “Baking Slide Settings” to adjust the baking time and temperature.

4. Select the option to limit manual reagent assignments.

a. Default is set to Unlimited.

b. Each test will count as 1 reagent assignment.

5. Select the option to automatically bake slides before staining.

6. Select the language setting for the software.

9.10.8 Network
Multiple Stainers may be linked together on a network to accommodate a shared label printer, main
server, LIM/LIS systems connection etc. Refer to 16.2. Setup Network

1. Click Network to setup the network configuration for the system.

9.10.9 LIM
The system must be individually configured for each customer site. Refer to 16.3. Setup LIS

Click LIM to configure the connection to the LIMS system.

MD-Stainer Service Manual V1._EN 44/173

 10 Maintenance
10.1 End-Customer Routine Maintenance
1. Daily Maintenance

a. Clean and dry chambers and module surfaces after each staining run.

i. Wipe the chamber surface with alcohol swabs immediately after removing
the stained slides.

ii. Use a soft paper towel to wipe away leftover reagents on the module,
especially in the area close to the hinge block.

b. (Preventative) Check for malfunctioning heaters after receiving a temperature

warning.

i. Click System Utilities > Tools > “Check Heaters” to check all 36 modules.

c. Empty the waste container.

2. Weekly Maintenance

a. Perform deep cleaning of chambers with bleach every 3-5 staining runs. Inspect
chambers for damage.

b. Perform tubing cleaning procedure. Inspect tubing for damage or build-up of residues.

c. Backup the report data if required.

d. (Preventative) Clean modules with water and mild detergent. Regular cleaning is
required to prevent excess salt build up. More frequent cleaning is required if ISH is
run due to excessive salt build up from the stringent wash.

3. Monthly Maintenance

a. Wipe the Z1/Z2 probe tips with an alcohol swab to remove accumulated salts and
other reagent residues.

b. Verify the SP1-Z1 and SP1-Z2 positions to ensure that there are no changes after
wiping the probe tips.

i. Click System Utilities > Tools > ”SP1-Z2 Calibration”.

ii. Verify that the probe tip is positioned as shown: X-center; Y back
center. The user may gently bend the probe back to the center if the position
is slightly off.

MD-Stainer Service Manual V1._EN 45/173

 iii. Click System Utilities > Tools > ”SP1-Z1 Calibration” and verify the position.

c. Wipe the wash station wells with an alcohol pad.

d. Clean and dry all instrument surfaces.

i. Visually check for liquid accumulated around the modules and deck plate
(recommended after every 20-30 staining cycles). Use a soft paper towel to
wipe away any liquid.

ii. Check the gaps around the modules and use a soft paper towel to absorb any
liquid.

e. (Preventative) Inspect chambers (at least monthly or every 50 runs) for cracks,
leaking, degradation of chamber surface and gasket.

f. (Preventative) Inspect modules and robot for loose screws and smooth operation.

g. (Preventative) Inspect tubing/hoses for damage or build-up of reagent waste

residues.

10.2 Technical Support Scheduled Routine Maintenance

It is recommended for Technical Support to perform maintenance every 6 months or 150-300 cycles
of staining.

10.2.1 Computer Maintenance

1. Run diagnostics on the system.

2. Remove old logs and data files

3. Scan the computer for viruses and eliminate as required.

4. Upgrade software and firmware

10.2.2 Cleaning and general inspection of the instrument

1. Clean with water and mild detergent the modules and dry module surfaces.

a. Wipe the chamber surface with alcohol swabs.

b. Use a soft paper towel to wipe away leftover reagents on the module, especially in
the area close to the hinge block.

c. Regular cleaning is required to prevent excess salt build-up. More frequent cleaning
is required if ISH is run due to excessive salt build-up from the stringent wash.

2. Empty the waste container.

MD-Stainer Service Manual V1._EN 46/173

 3. Perform a deep cleaning of chambers with bleach 1%.

a. Chamber Removal and Installation:

i. To remove the chamber, lift the lid up and gently press down on the back of
the chamber until it pops out of the lid.

ii. To insert the chamber, align the chamber with the lid and apply even force to
push up evenly on the chamber, until it snaps into place. Make sure the
chamber sits flat and all 4 ball plungers are holding the chamber in place.

Warning! Improper removal and installation of the chambers may

cause damage to the gasket. This may result in high background staining,
reduced staining area, or even negative staining.

b. Soak the chambers in a large volume of water for a minute to rinse off the bleach.

c. Use an alcohol swab to wipe the chamber surfaces clean.

d. Allow the chambers to air-dry (may use the soft paper towel).

4. Inspect chambers for damage or build-up of residues.

5. Wipe the Z1/Z2 probe tips with an alcohol pad to remove accumulated salts and other built
up residues.

6. Wipe the wash station wells with an alcohol pad.

7. Clean and dry the instrument.

a. Visually check for liquid accumulated around the modules and deck plate
(recommended after every 20-30 staining cycles)

b. Check the gaps around the modules and use a soft paper towel to absorb any liquid.

10.2.3 Tubing Cleaning Procedure

The Z1 and Z2 (waste) tubing may slowly build up DAB precipitate and other residues over time. Tubing
should be cleaned every 6 months (operating at 1 cycle a day) or 150 cycles of staining.

1. Fill two 15mL vials with the appropriate cleaning solution:

a. (Recommended) Use Bleach to remove DAB precipitate.

b. (Recommended) Use Slide Brite to remove wax residues.

2. Verify there is sufficient Wash Buffer in the wash bottle.

MD-Stainer Service Manual V1._EN 47/173

 3. Login to the main user interface and open System Utilities>Tools.

4. Click “Tubing Clean”.

5. Load the reagents onto the reagent rack and mount the rack onto the instrument.

6. Place Z1 tube cleaning solution on reagent rack position #1.

7. Place Z2 tube cleaning solution on reagent rack position #5.

8. Click “OK” to initiate the tube cleaning sequence. The Z1 and Z2 probes will both aspirate 5mL
of cleaning solution into the tubing from their respective reagent rack positions. The system
will then initiate a 20 minutes countdown.

9. After 20 minutes has elapsed, the system will automatically perform a system initialization
and purge the cleaning solution waste. The user may click “Cancel” at any moment to
immediately purge the waste from the tubing.

10. Inspect the tubing. There should be no visible wax residues, DAB precipitate or salt build-up.

11. Repeat the Tube Cleaning function as needed.

10.2.4 Components inspection

1. Inspect the tubing/hoses. It should appear clear and transparent. Perform the Tubing Cleaning
Procedure (see above) if the tubing appears brown or darkened.

a. New tubing should be installed when the residue can no longer be removed with the
Tubing Cleaning Procedure.

b. Disconnect the System Fluid and initialize the system 2 times in order to clear the
buffer from the line.

c. Plug the open ends of the tubing to prevent spilling liquid onto the instrument.

Warning! Do not spill liquid onto any exposed electrical parts/PCBs.

d. Replace the tubing and hoses if necessary.

e. After replacing the tubing, all system positions must be verified and re-calibrated (if
necessary).

2. Visually inspect the pump for salt crystals.

3. Clean the pump syringe:

a. Log on the system and make sure the system is initialized.

MD-Stainer Service Manual V1._EN 48/173

 b. Empty the buffer bottle.

c. Goto the System Utilities -> Tools

i. Use the “Prime Z1 and Z2” or “Prime Pump Z1” and “Prime Pump Z2” to dump
out all liquid in both syringes. You may need to do this several times.

ii. Once the syringes are empty, use “Replace Pump 1 Syringe” and “Replace
Pump 2 Syringe” to move the plungers of pumps to a lower position where
the syringes can be removed.

d. Remove the syringes.

i. Loose the plunger screw counter clockwise.

ii. Loose the syringe counter clockwise.

iii. After the syringe completely loose, push it downward to disconnect the
syringe with the valve, then remove it.

MD-Stainer Service Manual V1._EN 49/173

 e. Once the syringe removed from the pump, you can take the syringe and plunger apart
and use DI Water to clean then.

MD-Stainer Service Manual V1._EN 50/173

 f. After cleaned the plungers and syringe, reinstall them onto the pump.

Warning! When install the syringe to the valve, make sure it is NOT too tight, it
may deform the white plastic seal and the plastic valve, but also make sure that there is
not leak between the valve and syringe.

4. Unplug the power cable and wait a few minutes before checking the electrical parts.

a. Handle all electrical parts carefully if any of them need to be disconnected or

reconnected.

b. Visually inspect the PCB.

c. Carefully vacuum or blow away any dust or fine particles that have settled on the PCB.

Warning! Avoid directly touching any components on the PCB.

5. Check all cable connectors, and make sure they are securely tightened.

6. Check the chambers for damage to the gasket. Discard if necessary.

7. Inspect the robotic arm.

a. Inspect robot for loose screws and smooth operation.

b. Verity the robot calibration

c. Lubricate the XY and ZZ rail-styles if necessary.

d. Inspect and Clean the RFID Antenna.

8. Inspect and test all 36 modules.

a. Inspect modules and robot for loose screws and smooth operation.

b. Visually inspect the modules for smooth lid motion (up/down).

c. Click System Utilities>Check Heaters to verify heater function.

d. Replace modules or parts if necessary

10.2.5 Calibration
1. Verify the module calibration

2. Verify the Home position and Agitation Heights: Extract, A2, A5, A6, and A7. Recalibrate if
necessary.

MD-Stainer Service Manual V1._EN 51/173

 3. Calibrate the XYZ robot arm.

4. For a correct calibration please refer to the Service Manual chapter 4.3 Calibration: Module
Agitation Heights, document New IHC Protocol Template A3/A4 and document Calibration
Software Instructions.

10.2.6 Final tests

1. Confirm the changes by running a standard staining protocol.

MD-Stainer Service Manual V1._EN 52/173

 11 Module
Each instrument is equipped with 36 independent modules. Problem modules may be excluded from
the staining run without affecting the remaining modules, until a repair or replacement can be
performed.

11.1 Overview of Module Components

Part Quantit
Description Function Image
No. y

PAT-
Actuator PCB 1 Microprocessor for the module
PC302

PAT-
Heater 1 Accurate temperature control
PC001

PAT-
Chamber 1 Precise control of reagents on slide
PC700

PAT-
Slip Holder 1 Holds the chamber
PC015

PAT-
Ball Plunger 4 Secures chamber on slip holder
PC610

PAT-
Hinge Block 1 Holds slip holder
PC013

PAT- Linear step motor to control kinetic

Motor 1
PC351 motion

PAT- Push Rod with

1 Adapts between motor and slip holder
PC088 Flag

PAT-
O-Ring (blue) 1 Secures/seals push rod
PC623

MD-Stainer Service Manual V1._EN 53/173

 11.2 Recommended Staining Area

11.2.1 Staining Area Range

To ensure staining quality and reliability, tissue slides should be prepared following the staining area
guidelines for the MD-STAINER system. The yellow highlighted region is the recommended staining
area range. The circled area is the recommended tissue placement area. This area is achieved using
the standard 1mm slide, 130uL chambers and MD-Stainer default protocols and MD-Stainer default
agitation heights.

NOTE: The circular area around the chimney opening may be weaker or even negative due to
contact with the chimney base. Avoid placing tissues in this area.

11.2.2 MD_Stainer Tissue Slide Print Map

The tissue slide map may be printed for the user’s reference. It is recommended to use standard
75mmx25mmx1mm slides. Using slides of non-standard thickness may require module calibration.

MD-Stainer Service Manual V1._EN 54/173

 11.3 Calibration: Module Agitation Heights
During reagent incubation, the module lid will “agitate” between two different heights to improve the
rate of reaction while maintaining a uniform coverage area. This lid motion is termed “agitation”. Each
module is set with 9 defined agitation heights for this purpose: Extract/Inject, A1 to A7.

Home

A1

Inject/Extra
ct

A2

Down

11.3.1 Using the Slides Interface

1. Accessing the Slides Interface

a. Launch the PCStainer SW and login using a Distributor-level account.

b. Click the icon on the Windows task bar to display Autostainer Server UI.
Alternatively, open C:\PathCom\PathComAutostainer\ and run
PathComAutostainer.exe

MD-Stainer Service Manual V1._EN 55/173

 c. Click the Slides tab and click “Connect” to open communications with the slides
processor

2. Selecting a Module or Group of Modules

a. Input the Device Address of a module 1-36 to select an individual module

b. Check the box Group to select a group of modules

c. Check the box Broadcast to select all 36 modules

3. Reporting

a. Data stored in the module can be read by the user

i. Select a parameter from the dropdown list i.e.: Home Position, Motor
Position, Current Temperature etc.

ii. Click “Get” to read the data in the box to the left

b. Click “E Vals” to view the current agitation heights of the module

c. Click “SNR” to view the serial number of the module

MD-Stainer Service Manual V1._EN 56/173

 4. Move to Fixed Position

a. Move the lid “Home”, “Down” or one of the 9 defined agitation heights

i. Select a position and click “Go” to move the lid to the defined height

5. Lid Move

a. Move the lid a relative number of steps up

i. Select “Up” and input the number of Steps

ii. Click “Go” to lift the lid from the current position

b. Move the lid a relative number of steps down

i. Select “Dn” and input the number of Steps

ii. Click “Go” to lower the lid from the current position

6. Position Definitions (Set to Current)

a. Save the current position to a defined position

i. Select “Home”, “Down” or one of the 9 defined agitation heights

ii. Click “Set” to save the current position to the defined position

7. Agitation (“Run” Sets Values as Defaults)

a. The user may set an agitation cycle to verify agitation heights of a module

i. Input the Upper Lid Position (steps) i.e.: Inject/Extract, A2, A3, and A4 which
will determine the absolute height that the lid will travel upwards

ii. Input the Lower Lid Position (steps) i.e.: A5, A6, A7, Down which will
determine the absolute height that the lid will travel downwards

iii. Set the Lid Time (seconds) at the Upper and Lower Positions

iv. Set the number of Cycles

v. Click “Run” to begin agitation

11.3.2 Calibrating the “Home” Position

Each module is set to “overdrive” about 10-15 steps. This is observed when the motor produces 4±1
“clicks” when the module lid moves from the “Home” to the “Down” position.

11.3.2.1 Verifying the “Home” Position

1. Lift the module lid to the “Home” position, insert a standard 1mm slide, and go “Down”.

MD-Stainer Service Manual V1._EN 57/173

 2. Count the number of “click” sounds produced by the motor. The “Home” position may need
to be adjusted if the number “clicks” exceeds the ideal range of 3-5 “clicks”.

a. When the motor “overdrives” too many steps, the lid may press down with too much
force and cause damage to the motor and module components.

b. When the motor “overdrives” too many steps, the lid may press down with too much
force and cause damage to the motor and module components.

NOTE: 1 “click” = 4 steps.

11.3.2.2 Adjusting the “Home” Position

1. If more than 5 “clicks” are heard, the “Home” position step # is too large.

a. Lift the lid back to “Home”.

b. Move the lid down the calculated # of steps:

i. Relative # of Steps Dn = (# of “clicks” heard – 4 “clicks”) x 4

c. Save the new “Home” position.

d. Lift the lid to “Home” again and go “Down” to confirm the number of clicks.

e. Repeat the above steps as needed.

2. If fewer than 3 “clicks” are heard, the “Home” position step # is too small.

MD-Stainer Service Manual V1._EN 58/173

 a. Proceed as directed above.

b. Move the lid up the calculated # of steps:

i. Relative # of Steps Up = (# of “clicks” heard – 4 “clicks”) x 4

11.4 Troubleshooting: Module

11.4.1 Symptom: Module lid is stuck.

The lid cannot move from the up or down position.

1. Cause: The moving components of the module have become misaligned (may happen if
module has been left in the “Down” position for a long time).

Solution: Perform the Self Alignment Check.

2. Cause: Actuator PCB malfunction (the lid movement may reverse direction or recover after
going to the “Down” position”).

Solution: Replace the Actuator PCB.

3. Cause: The O-ring around the push rod has expanded. The push rod cannot move smoothly
up/down.

Solution: Replace the O-ring.

4. Cause: Motor failure (rare).

Solution: Replace the Motor.

5. Cause: The Push Rod has become slightly bent (caused by too much overdrive of motor at
Home position).

Solution: Replace the Push Rod.

MD-Stainer Service Manual V1._EN 59/173

 11.4.2 Symptom: Module stammer.
The lid does not move up and down smoothly.

1. Cause: The moving components of the module have become misaligned.

Solution: Perform the Self Alignment Check.

2. Cause: The O-ring around the push rod has expanded. The push rod cannot move smoothly
up/down.

Solution: Replace the O-ring.

3. Cause: Friction build up on module moving parts.

Solution: Reapply silicone lubricant around hinge and/or push rod.

11.4.3 Symptom: Module No Reply error.

1. Cause: The “gold finger” connectors on the actuator PCB are dirty.

Solution: Clean the “gold fingers” with high proof alcohol solution.

2. Cause: The backplane PCB connector slot is dirty.

Solution: Spray some compressed air into the connector on the backplane PCB to dislodge
dust/debris.

Use a small disposable pipette to flush the connector on the backplane PCB with high proof
alcohol solution if necessary.

3. Cause: The actuator PCB has poor contact with the connector slot.

Solution: Remove and reinstall the module (the light should be green). Swap slot positions
with a different module.

4. Cause: Actuator PCB failure.

Solution: Replace the Actuator PCB.

5. Cause: The Backplane PCB connector slot is damaged.

Solution: The Backplane PCB must be repaired and/or replaced.

11.4.4 Symptom: Module goes to an unexpected agitation position.

1. Cause: The PCB has lost the calibration data for the agitation position (eval has spontaneously
changed to a new number/undefined 4-digit number).

Solution: Verify firmware version. Resave the calibration data. Replace the actuator PCB if
necessary.

MD-Stainer Service Manual V1._EN 60/173

 2. Cause: The motor has lost the Home position during the run.

Solution: Verify that the flag is seated firmly on the push rod. Verify that the push rod is fully
tightened to the motor. Verify that the flag is lined up with the sensor on the actuator PCB.
Remove dust/debris around the sensor. Replace the PCB or Motor or Push Rod if necessary.

3. Cause: Debris is stuck on the slide and prevents the lid from going down completely.

Solution: Clean up the area around the hinge block and around the slide.

4. See above, Module lid is stuck.

5. Cause. Motor failure.

Solution: Replace the Motor.

11.4.5 Symptom: Chamber inserts unevenly.

1. Cause: Broken or loose ball plunger.

Solution: Remove the chamber and inspect the ball plungers on the slip holder (2 on each
side). The ball may have broken loose from the plunger. Replace the Ball Plunger.

11.4.6 Symptom: Slide does not insert into the module.

1. Cause: Salt has accumulated around the springs/plastic dowel pins.

Solution: Place the module standing up vertically, with the motor bracket side down. Apply
water to the slot and wait for a while to allow the salt to dissolve/loosen. If water is not
effective, apply WD-40. Clean the hinge block.

2. Cause: Glass, salt and reagent debris has accumulated around the hinge block.

Solution: Use a paper clip or small tool to clear the debris from the slot.

3. Cause: Module base plate bowed slightly (slide can be inserted when the module is removed
from the deck plate).

Solution: Try to push down on the backplane PCB to lower it. Slightly sand the edge of the
actuator PCB to allow it to sit higher up on the bracket and adjust to bias toward the motor
bracket. Adjust the bend of the PCB bracket.

4. Cause: Heater is too high.

Solution: Shim Up the Hinge Block or Replace the Heater.

5. Cause: Non-standard glass slide or front clip is too long.

Solution: Loosen the two screws on the front clip. Sand/cut the front clip shorter to
accommodate longer slides.

MD-Stainer Service Manual V1._EN 61/173

 11.4.7 Symptom: Module displays persistent Overheating and/or Low Temperature
warning during runtime.
1. Cause: Too much liquid has accumulated around the heater plate.

Solution: Carefully clean around the module base plate, hinge block and heater plate.

2. Cause: Heater sensor failure. Fails to heat to the correct temperature.

Solution: Replace the Heater.

11.4.8 Symptom: Module fails the routine heater check.

1. Cause: Heater failure. Fails to heat up.

Solution: Replace the Heater.

2. Cause: Heater sensor failure. Fails to heat to the correct temperature.

Solution: Replace the Heater.

3. Cause: Actuator PCB failure (broken communications connection).

Solution: Replace the Actuator PCB.

11.4.9 Symptom: Cannot connect to the Slides.

1. Cause: COM Port assignment changed or unavailable.

Solution: Restart the computer to recover the COM Ports. Change the COM Port number if it
is not a number between 2 and 9.

2. Cause: Backplane board connection issue.

Solution: Verify that the Internet cable is securely connected to the Communications board
and the Backplane PCB.

3. Cause: Backplane board power issue. Module lights do not turn on.

Solution: Verify that the power supply cable is undamaged and securely connected to the
Power Supply and the Backplane PCB.

4. Cause: Communications board failure.

Solution: Replace the Communications board.

5. Cause: Backplane PCB malfunction.

Solution: Replace the Backplane PCB. Not recommended. Consult MD-Stainer Technical
Support.

MD-Stainer Service Manual V1._EN 62/173

 11.5 Maintenance/Repair: Module

11.5.1 Chamber Cleaning and Replacement

Residues from the staining run will build up on the chamber surface. Chambers must be cleaned and
inspected regularly to preserve staining quality.

1. Remove/Replace the Chamber

a. To remove the chamber, lift the lid up and gently press down on the back of the
chamber until it pops out of the lid.

b. To insert the chamber, align the chamber with the lid and apply even force to push up
evenly on the chamber, until it snaps into place. Make sure the chamber sits flat and
all 4 ball plungers are holding the chamber in place.

Warning: Improper removal and installation of the chambers may cause

damage to the gasket. This may result in high background staining, reduced staining
area, or even negative staining.

2. Clean the Chamber

a. Clean the chambers as needed when residues have built up on the chamber surfaces.

Before deep cleaning with bleach

(Surface is visibly darkened/stained with

DAB/Hematoxylin residue)

After deep cleaning with bleach

b. Perform “Deep Cleaning” with bleach every 3-5 staining cycles (recommended).

i. Remove chambers from the instrument (see below, Chamber Removal and
Installation).

ii. Soak and stir the chambers in regular bleach (available at the grocery store)
for about 15-30 minutes, depending on concentration of bleach.

MD-Stainer Service Manual V1._EN 63/173

 iii. Gently wipe away any remaining DAB residues on the chamber and gasket.

iv. Check the chambers for damage to the gasket. Discard if necessary.

v. Soak the chambers in a large volume of water for a minute to rinse off the
bleach.

vi. Allow the chambers to air-dry (may use the soft paper towel).

vii. Use an alcohol swab to wipe the chamber surfaces clean.

Warning: Never leave the chambers in the bleach overnight. This will severely damage
the chambers. The maximum recommended bleaching time is 30 minutes.

c. (Alternative option) Run the “Clean Chamber” protocol on the instrument every 3-5
staining cycles (recommended).

NOTE: “Deep Cleaning” can be performed every 10-15 staining cycles if running
“Clean Chamber” protocol regularly.

i. Insert empty slides into the modules, and load the MD-Stainer Chamber
Cleaning Kit onto the reagent rack. Refer to the data sheet for more specific
details.

ii. The protocol will take approximately 2.5 hours to clean 36 slides.

11.5.2 Module Replacement

In the event of module failure/malfunction, it is advised to replace the module on-site. The problem
module may be returned to the service facility or MD-Stainer for diagnosis, testing and repair.

MD-Stainer Service Manual V1._EN 64/173

 1. Remove the module from the deck plate

a. Lift the module lid to the Home position. Clean up any liquids remaining on the
module surface.

b. Unscrew the 4 corner screws.

c. Power off the instrument before removing the module to prevent damage to the PCB.

d. Grasp the lid and pull up. Be careful not to drip any liquid onto the backplane or
actuator PCB.

2. Install the module onto the deck plate

a. Replace the Rectangular O-ring with a new one if it appears damaged, deformed or
the seal is broken.

b. Make sure that the O-ring sits evenly and flat in the slot on the deck plate.

c. Insert the module into the slot. The module base plate should lock with the
registration pin and the “gold fingers” should line up with the connector on the
backplane PCB.

d. Power the instrument on and verify the connection (green light).

e. Tighten the 4 corner screws with even force

f. If the module is swapped or re-assembled, verify the Z1 and Z2 calibration. Verify the
Home position and agitation heights. Recalibrate as needed.

3. Replace the Rectangular O-Ring

a. Replace the used O-ring with a new O-ring before installing the module back onto the
instrument.

MD-Stainer Service Manual V1._EN 65/173

 b. Use a cover i.e.: tape/paper to prevent liquid from dropping into the connectors on
the backplane.

c. Clean up any reagent residue on the deck plate.

i. Make sure to clean the area under the deck plate.

ii. Clean up the O-ring recess area with 100% alcohol.

d. Insert the O-ring into the O-ring recess and check the fit.

e. Install the module onto the instrument.

f. Lubricate the 4 screw holes on the deck plate and/or lubricate the screws before
tightening.

11.5.3 Module Repair

1. Perform the Self Alignment Check

a. Remove the module and loosen the two screws securing the motor to the motor
bracket.

b. Visually check the push rod alignment and lubrication etc.

c. Verify that the push rod can move smoothly up/down.

d. Return the module to the instrument, and go “Home” and “Down” several times to
perform self-alignment.

e. Move the lid back to the "Home" position and remove the module from the
instrument.

f. Re-tighten the 2 screws on the motor bracket while holding the module lid fixed to
maintain alignment. Press down on the lid with the index and middle finger while
holding the base with the thumb.

MD-Stainer Service Manual V1._EN 66/173

 g. Return the module to the instrument. Set it to agitate several times and set it down
to verify module function.

2. Perform the “Quick” Parallel Check

a. Go to the “Home” position.

b. Insert a 43mm slide and a chamber into the module.

c. Go to the “Down” position.

d. Check for any gaps along the gasket seal using a flashlight.

e. If a gap is visible on the FRONT left or right, then the hinge block must be shimmed up
on that side only.

f. If a gap is visible on the entire FRONT, then the hinge block must be shimmed up on
both sides.

g. If a gap is present on the BACK (close to the hinge), then the heater is too low.

NOTE: To inspect the BACK, remove the module from the instrument
and then remove the left and right-side rails. Hold the module up against the
overhead lighting to check for gaps.

MD-Stainer Service Manual V1._EN 67/173

 3. Lubricate the Module Parts

a. Use a very small amount of silicone O-ring lubricant to lubricate the module moving
parts as needed during repair/service.

i. Push Rod

ii. Compressed Spring (2 Springs in Hinge Block)

iii. Dowel Pin (through Slip Holder and Hinge Block)

iv. Shoulder Screw (on Slip Holder)

4. Replace the Actuator PCB

a. Remove the module and unscrew the two screws securing the PCB to the PCB bracket.

b. Disconnect the PCB from the motor and heater. Cut the cable tie securing the wires.

i. Heater wires: RED RED WHITE WHITE

ii. Motor wires: BLACK RED BLUE GREEN

c. Replace the PCB with a new PCB. Verify that the PCB is positioned perpendicular to
the base plate and sits flat on the PCB bracket. Before tightening the screws, bias the
PCB towards the motor bracket.

d. Connect the new PCB to the motor and heater.

e. Return the module to the instrument.

MD-Stainer Service Manual V1._EN 68/173

 f. Verify the connection (the light should be green).

g. Verify that the firmware is up-to-date.

h. Save the serial number Device SNR.

i. Save the Home Position.

j. Save the agitation heights.

k. Verify the agitation positions. Recalibrate the module if necessary.

5. Replace the Motor: Not recommended.

a. Replace the module and return to Manufacturer for service.

6. Replace the Push Rod: Not recommended.

a. Replace the module and return to Manufacturer for service.

7. Replace the O-Ring: Not recommended.

a. Replace the module and return to Manufacturer for service.

8. Replace the Heater: Not recommended.

a. Replace the module and return to Manufacturer for service.

9. Shim Up the Hinge Block: Not recommended.

a. Replace the module and return to Manufacturer for service.

10. Clean the Hinge Block: Not recommended.

a. Using a hex head tool, unscrew the 2 set screws on the back of the hinge block.

b. Using a small blunt tool, push on the plastic dowel pin from the slotted side of the
hinge block. The spring and plastic dowel pin should slide out of the hole.

c. Clean up the holes, compression springs and dowel pins then reapply lubricant as
needed.

d. Reinsert the dowel pins and springs and secure with the set screws.

MD-Stainer Service Manual V1._EN 69/173

 11. Replace the Hinge Block: Not recommended.

a. Replace the module and return to Manufacturer for service.

12. Replace the Ball Plunger

a. Lift the module lids to the “Home” position.

b. Lower all other module lids to the “Down” position.

c. Remove the chamber.

d. Unscrew the ball plunger and replace with a new ball plunger. Verify that it is even
with the other ball plungers along the inside edge of the slip holder.

e. Reinsert the chamber. Verify that the ball plunger is not too loose/too tight. The
chamber should clip on easily.

13. Replace the Slip Holder: Not recommended.

a. Replace the module and return to Manufacturer for service.

14. Replace the Front Clip

a. Unscrew the two screws securing the front clip to the module base plate.

b. Replace with a new front clip. Do not over-tighten the screws.

c. Verify that the slide can be inserted and removed easily without popping up or
damaging the edges.

MD-Stainer Service Manual V1._EN 70/173

 12 Robot
The robot is equipped with an XYZ arm with two Z axes:

The X axis mechanism enables the X arm to move from left to right across the instrument.

The Y axis mechanism is the robotic arm extending from the front to the back of the instrument,
carrying the Z head assembly. The Y arm moves from right to left across the instrument.

The Z head assembly sits over the Y arm and moves from front to back across the instrument.

1. Z1 extracts the reagent from the reagent vial and injects it into the chamber. It also supplies
in-line wash buffer.

2. Z2 extracts the reagent waste from the chamber.

12.1 Overview of Robot Components

Part No. Description Quantit Function Image
y

PAT-PC760 X Optical Sensor 1 X optical home sensor

PAT-PC761 X Motor 1 X stepper motor

PAT-PC762 XYZ Communication Cable 1 Connects Interconnect to

Communications board

PAT-PC763 Flat Flex Cable, 10 POS, 20" 1 Connects LLD sensor to

YZZ Opto

PAT-PC764 Liquid Level Sensor 1 Detects liquid level of

reagent

PAT-PC765 PCBA Controller/Driver for 1 Z2 motion controller

Z2 Axis

MD-Stainer Service Manual V1._EN 71/173

 PAT-PC766 YZZ Opto PCB 1 Y, Z1, Z2 optical home
sensors

PAT-PC767 Motor Interface PCB for 1 Interface for power and

XYZZ communications from Z1
and Z2 motion controllers
to YZZ Opto

PAT-PC768 CCU for XYZZ 1 CCU translator board

PAT-PC769 XYZ Controller PCB 1 YZZ motion controller

1 X motion controller

PAT-PC770 Cable Set, X Flex 16 POS, 1 Connects X Controller to

40/30" Interconnect and YZZ
Controller to
Interconnect

PAT-PC771 Cable Set, Y Flex 10 POS, 24" 1 Connects YZZ Opto to

Motor Interface and YZZ
Opto to YZZ Controller

PAT-PC773 Z2 Opto Cable 1 Connects YZZ Controller N/A

to Z2 Controller

PAT-PC774 Z2 Motor Cable 1 Connects Z2 Controller to N/A

Motor Interface

PAT-PC775 Interconnect PCB 1 RS232 interface for power N/A

and communications to
controller boards

PAT-PC777 Vmot/485 Cable to J4 1 Connects YZZ Controller N/A

to Z2 Controller (power
and communications)

12.2 Extraction
Precise calibration of the XYZZ axes is essential to staining quality and consistency. Partial extraction
or failure to extract reagent waste can produce weaker or even negative test results. To test the
calibration of the XYZZ robot, the user may perform a reagent extraction test.

MD-Stainer Service Manual V1._EN 72/173

 12.2.1 Reagent Inject and Extract Test

1. Login to the main user interface .

2. Clean and dry all 36 chambers. Insert clean 1mm slides.

3. Load one vial of DS1a into the reagent rack (enough for 36 tests).

4. Run the “Extracting Test” and observe the following:

a. Aspirate reagent from reagent vial.

i. The Z1 probe should take the reagent from the center of the bottle, without
hitting the bottom or any part of the reagent vial.

b. Inject reagent into the 36 modules.

i. The Z1 probe hits the chamber chimney at the center without bending the
chimney or chamber gasket too much.

ii. The injected reagent does not overflow from the chimney.

iii. The injected reagent spreads smoothly onto the slide.

c. Extract waste from the 36 modules.

i. The Z2 probe hits the chamber chimney at the center without bending the
chimney or chamber gasket too much.

ii. The reagent waste is extracted cleanly.

NOTE: A small dot of residual waste collected below the chimney is

acceptable.

5. Make adjustments to the calibration if needed.

a. Before making any adjustments to the calibration values, verify that the Z1 and Z2
probes are not bent.

i. Click System Utilities > Tools > SP1-Z2 Calibration. Verify that the Z2 probe is
centered toward the back of the chimney opening.

ii. Click System Utilities > Tools > SP1-Z1 Calibration. Verify that the Z1 probe is
centered toward the back of the chimney opening.

b. Verify the XYZ positions and adjust the offsets in the correction table.

MD-Stainer Service Manual V1._EN 73/173

 c. Adjust Extract/Inject position.

d. Adjust defined vertical positions: SP-Z1 and SP-Z2.

i. SP-Z1 is about 100 steps lower than XY Adjust Z1.

ii. SP-Z2 is about 90 steps lower than XY Adjust Z2.

NOTE: The actual value may range between 80 and 100 steps,
depending on the module tilt angles for extracting.

6. Retest the injection/extraction until each module has consistent and clean extraction.

7. (Optional) Test the margin of error for injection/extraction.

a. Change SP-Z1 and SP-Z2 to 10 steps higher, and run the Extracting Test.

b. Change SP-Z1 and SP-Z2 10 steps lower, and run the Extracting Test.

c. Adjust SP-Z1 and SP-Z2 as needed based on the test results.

MD-Stainer Service Manual V1._EN 74/173

 12.2.2 Troubleshooting: Robot
Always contact MD-Stainer Technical Support for assistance with robot malfunction/errors.

Replacement of boards and cables is not recommended without thorough training by Manufacturer
and review of all diagrams. Improper handling of cables may result in damage. Accidental
misconnection of cables on the electronic boards may result in permanent damage to the Robot.

Before proceeding with troubleshooting, please verify the 1) communications connections, 2) power
connections and 3) system settings for the robot.

12.2.3 Symptom: Probe is bent or off the original calibrated positions.

a. Cause: Accidental collision with an improperly placed reagent vial/obstruction in the XYZZ
plane. Robot XY or ZZ error (rare).

Solution: Bend the probe back to the center position.

b. Cause: Computer lost all calibration data and system settings.

Solution: Refer to 17.3.1. Symptom: Computer lost all calibration data and system settings.

c. Cause: X, Y, Z1 or Z2 malfunction (may be intermittent) causes collisions with module deck,

wash stations and or reagent rack.

MD-Stainer Service Manual V1._EN 75/173

 Solution: Consult MD-Stainer Technical Support if the error occurs repeatedly.

12.2.4 Symptom: Cannot connect to the Robot.

a. Cause: COM Port assignment changed or unavailable.

Solution: Restart the computer to recover the COM Ports. Change the COM Port number if it
is not a number between 2 and 9.

b. Cause: Robot connection issue.

Solution: Verify that the Robot Communications cable is undamaged and securely connected
to the Communications board and the Interconnect PCB.

c. Cause: Robot power issue. LED lights on the electronic boards are off.

Solution: Verify that the 12-24V Power Converter cable is undamaged and securely connected
to the 12-24V Power Converter cable and the Interconnect PCB.

d. Cause: Communications board failure.

Solution: Replace the Communications board.

e. Cause: 12-24V Power Converter failure.

Solution: Replace the 12-24V Power Converter.

f. Cause: Interconnect PCB failure.

Solution: Consult MD-Stainer Technical Support. (Not recommended) Replace the

Interconnect PCB.

12.2.5 Symptom: Cannot initialize the Robot.

a. Cause: Robot was powered off in the middle of an operation. Timeout awaiting reply.

Solution: Restart the Autostainer Server.

b. Cause: Z2 Device Address was changed.

Solution: Close the Autostainer Server to restore the address. Verify all Device Addresses in the
Robot > Setup tab.

c. Cause: Initialization error of Z2, Z1, X, Y or Z1 and/or Z2 pump.

Solution: Determine the source of the problem by disabling the devices one at a time using the
server.

i. Under Robot > Setup, uncheck only the box next to Device A. Click “Save
Configuration” and click “Initialize”. The Z1 pump should be disabled.

MD-Stainer Service Manual V1._EN 76/173

 ii. Under Robot > Setup, uncheck only the box next to Device B. Click “Save
Configuration” and click “Initialize”. The Z2 pump should be disabled.

iii. Under Robot > Setup, uncheck only the box next to Device Z1. Click “Save
Configuration” and click “Initialize”. The Z2 axis should be disabled. See below for
further details.

iv. If the error does not repeat after Z1/Z2 pump and Z2 axis are disabled, then there
is a problem with XYZZ axis. See below for further details.

d. Cause: Timeout error.

Solution: See below for further details.

12.2.6 Symptom: Z2 and/or Z1 initialization error.

a. Cause: Z sensor or flag problem.

Solution: Verify that the Z flag does not obstruct the sensor at the Home position. Carefully blow
away any dust/debris that may be obstructing the laser sensor.

b. Cause: Intermittent or broken connection on crimp terminal cables.

Solution: Inspect all cable connections. Cable wires should have good contact to crimp terminals.

i. (For Z1 only) Verify that the Z1 Motor cable is undamaged and securely connected
to the YZZ Controller and the Motor Interface.

ii. (For Z2 only) Verify that the Z2 Motor cable is undamaged and securely connected
to the Z2 Controller and the Motor Interface.

iii. (For Z2 only) Verify that the Z2 Opto cable is undamaged and securely connected
to the YZZ Controller and the Z2 Controller.

iv. (For Z2 only) Verify that the Vmot/485 cable is undamaged and securely
connected to the YZZ Controller and the Z2 Controller.

c. Cause: Intermittent or broken connection on the flat flex cables.

Solution: Inspect all cable connections. Flex cables should move freely without obstructing the YZZ
axes.

i. Verify that the Y flex cable (top) is undamaged and securely connected to the YZZ
Opto and the YZZ Controller.

ii. Verify that the Y flex cable (bottom) is undamaged and securely connected to the
YZZ Opto and the Motor Interface.

d. Cause: YZZ Controller problem.

MD-Stainer Service Manual V1._EN 77/173

 Solution: Consult MD-Stainer Technical Support. (Not recommended) Replace the YZZ Controller
board.

e. Cause: (For Z2 only) Z2 Controller problem.

Solution: Consult MD-Stainer Technical Support. (Not Recommended) Replace the Z2 Controller
board.

f. Cause: YZZ Opto problem.

Solution: (Not recommended) Replace the YZZ Opto.

g. Cause: Motor Interface problem.

Solution: (Not recommended) Replace the Motor Interface.

12.2.7 Symptom: X initialization error.

a. Cause: X sensor or flag problem.

Solution: Verify that the X flag does not obstruct the sensor at the Home position. Carefully blow
away any dust/debris that may be obstructing the laser sensor.

b. Cause: X encoder problem. LED on X Controller board is flashing.

Solution: Verify the connection of the X encoder to the X Controller Board and the X Motor.

c. Cause: X Controller problem.

Solution: Consult MD-Stainer Technical Support. (Not recommended) Replace the X Controller
board.

12.2.8 Symptom: Y initialization error.

a. Cause: Y sensor or flag problem.

Solution: Verify that the Y flag does not obstruct the sensor at the Home position. Carefully blow
away any dust/debris that may be obstructing the laser sensor.

b. Cause: Y encoder problem. LED on YZZ Controller board is flashing.

Solution: Verify the connection of Y encoder to the YZZ Controller Board and the Y Motor.

c. Cause: YZZ Opto problem.

Solution: Verify that the Y flex cable (top) is undamaged and securely connected to the YZZ Opto
and the YZZ Controller. (Not recommended) Replace the YZZ Opto.

d. Cause: YZZ Controller problem.

MD-Stainer Service Manual V1._EN 78/173

 Solution: Consult MD-Stainer Technical Support. (Not recommended) Replace the YZZ Controller
board.

12.2.9 Symptom: Z2 and/or Z1 do not respond.

a. Cause: Unexplained error on Z2.

Solution: Restart the Autostainer Server. Verify that the Device Address Setting on Z2 is set to 11
on the Robot > Setup tab.

b. Cause: Physical obstruction/resistance on the ZZ axes.

Solution: Verify that the ZZ axes can move smoothly. Lubricate the rail styles (if necessary).

c. Cause: Cable connection or board problem.

Solution: Refer or further troubleshooting to 12.2.6. Symptom: Z2 and/or Z1 initialization error.

Symptom: X and/or YZZ axes does not respond.

a. Cause: Robot power or connection issue. LED lights on one or more electronic boards are off.

Solution: Verify that the X and/or Y Flex cables are undamaged and securely connected to 1) the
Interconnect PCB and the YZZ Controller board and 2) the Interconnect and the X Controller board.

12.2.10 Symptom: X or Y axes does not respond or responds intermittently.

a. Cause: Physical obstruction/resistance on the XY axes.

Solution: Verify that the X or Y axes can move smoothly. Lubricate the rail styles (if necessary).
Check the belt.

b. Cause: Encoder problem. LED light on controller board may be flashing.

Solution: Please contact Manufacturer for further support.

c. Cause: Wrong signal sent to X or YZZ Controller board.

Solution: Fully power-off the instrument to recover X or Y function. Verify that the correct number
of jumpers is installed on the controller board.

d. Cause: Controller board problem.

Solution: Consult MD-Stainer Technical Support. (Not recommended) Replace the X or YZZ
Controller board.

e. Cause: Interconnect PCB problem.

Solution: Consult MD-Stainer Technical Support. (Not recommended) Replace the Interconnect
PCB.

MD-Stainer Service Manual V1._EN 79/173

 12.2.11 Symptom: LLD Sensor false negative detection. Reagent volume in vial is not
detected.
a. Cause: Reagent cannot be detected by LLD Sensor.

Solution: None. Some reagents cannot be detected due to low conductivity.

b. Cause: LLD connection issue. System fails to detect all reagents/known detectable reagents.

Solution: Verify that the Y Flex cable (top) is undamaged and securely connected to the YZZ
Controller and the YZZ Opto board. Verify that the Flat Flex cable is undamaged and securely
connected to the YZZ Opto and the LLD Sensor.

c. Cause: Poor grounding. System fails to detect all reagents/known detectable reagents.

Solution: Verify that the LLD Sensor board has good contact to the rack extrusion. Verify that
the reagent rack support plane is grounded.

d. Cause: LLD Sensor problem. System fails to detect all reagents/known detectable reagents.

Solution: Replace the LLD Sensor board.

12.2.12 Symptom: LLD Sensor false positive detection. Reagent volume remaining in
vial is greater than expected.
a. Cause: Poor grounding. System detects empty/known undetectable reagents.

Solution: Verify that the LLD Sensor board has good contact to the rack extrusion. Verify that
the reagent rack support plane is grounded.

b. Cause: LLD Sensor problem. System detects empty/known undetectable reagents.

Solution: Replace the LLD Sensor board.

12.3 Maintenance/Repair: Robot

Repairs/modifications to the robot should not be made without proper training/assistance from
Manufacturer support. Improper handling of the robot may result in irreversible damage to its
components. Never attempt to perform repairs on the Robot while the instrument is still powered on.

12.3.1 Bend Probe Z1 or Z2

a. Run SP1-Z1 Calibration or SP1-Z2 Calibration from System Utilities > Tools

b. Verify SP1-Z1 or SP1-Z2 at module position 1.

The probe tip should be positioned at the X-center; Y back center

c. Bend the probe back to the correct position if necessary.

MD-Stainer Service Manual V1._EN 80/173

 12.3.2 Lubricate the Rail-Style
a. Apply a few drops of lubricant on both rails of the X axis.

i. Only use lubricant specially designed for rail-style systems.

b. Move the arm left-right several times to distribute the lubricant.

c. Apply lubricant to rails on the Z1 and Z2 axes.

d. Move Z1 and Z2 axes up and down to distribute the lubricant.

12.3.3 Clean the Optical Sensor

a. Use compressed air to dislodge dust/debris from the optical sensor.

12.3.4 Replace the LLD Sensor Board.

a. Clear the buffer line.

b. Power off the instrument. Manually move the Z1 axis up.

c. Unscrew the collet cap.

d. Slide the collet cover down and off of the collet.

e. Pull down on the tubing and remove the probe. Blot away any remaining liquid. Do not allow
any liquids to contact the electronic components.

f. The LLD board is secured around the tubing by the probe tab. Pull the tubing up slightly to
free the LLD board.

g. Slide the LLD board out of the collet. Unlock the flex cable.

h. Insert the flex cable into the connector on the new LLD board and lock it in place. Make sure
to fold the excess length of flex cable the same way as before.

MD-Stainer Service Manual V1._EN 81/173

 i. Install the LLD board onto the collet. Refer to robot manufacturer’s instructions for more
details.

j. Slide the collet cover back onto the collet.

k. Pull down the tubing and insert the probe.

l. Recalibrate XYZ for Z1.

m. Test the LLD function. Make sure the wash buffer is connected.

i. Use wash buffer or any ionic liquid to test for positive detection.

ii. Use an empty vial to verify negative detection.

12.3.5 Replace the <?> Board or <?> Cable on the Robot.

Replacement of boards and cables on the robot is extremely risky and not recommended.

Consult Manufacturer before attempting any repairs.

Robot failures must be handled on a case-by-case basis. Review and follow all manufacturers’
instructions. Proceed with caution.

Y Flex
Y Flex

MD-Stainer Service Manual V1._EN 82/173

 12.3.6 Verify the Dip Switch Settings on the Interconnect Board
a. Slide the X Cover out after unscrewing the 4 screws at the base.

b. Verify the Dip Settings on the Interconnect according to the figure below.

i. 10-pin dip switch: DOWN (1, 2, 5, 6, 7, 8) and UP (3, 4, 9, 10)

ii. 4-pin dip switch: DOWN (1) and UP (2, 3, 4)

NOTE: Also verify the Dip Switch Settings on all replacement boards before installing.

12.3.7 Verify the Jumper Configuration on the XYZ Controller Board

a. Remove the Back panel to access the X Controller Board.

b. There should be two jumper locks on the J2 jumper pins as shown in the figure above.

i. 5-pin jumpers: Unlocked (1, 2, 5), Locked (3, 4)

NOTE: 1 is farthest inside the instrument and 5 is closest to Back Panel.

MD-Stainer Service Manual V1._EN 83/173

 13 RFID Reader
13.1 Overview of RFID Components
Part No. Description Quantit Function Image
y

PAT- RFID Ribbon Cable 1 Connects RFID Reader

PC316 Adapter A to Adapter B

PAT- RFID Adapter A 1 Adapter for RFID Module

PC305 and RFID Ribbon Cable

PAT- RFID Adapter B 1 Adapter for Fans, RFID

PC306 Ribbon Cable and RFID
Communications Cable

PAT- RFID Communications Cable 1 Connects RFID Reader

PC308 Adapter B to
Communications board

PAT- RFID Module 1 Interprets radio

PC320 frequency signals

PAT- RFID Antenna 1 Emits and detects radio

PC321 frequency signals

13.2 Troubleshooting: RFID Reader

13.2.1 Symptom: RFID Reader is not reading/writing all tags

a. Cause: RFID Port is not connected.

Solution: Verify that the USB is connected to the designated port on the computer. Restart
the computer.

b. Cause: RFID Reader XYZ position is not calibrated.

Solution: Recalibrate RFID-R1. Adjust the RFID Reader height.

c. Cause: RFID Antenna is disconnected.

MD-Stainer Service Manual V1._EN 84/173

 Solution: Verify the connection between the RFID Antenna cable and the port on the RFID
Module.

d. Cause: Damage to the RFID Antenna/Module.

Solution: Replace RFID Antenna/Module.

13.2.2 Symptom: RFID Reader is not reading/writing one or a few tags

a. Cause: RFID reader XYZ position is not calibrated.

Solution: Recalibrate RFID-R1. Adjust the RFID Reader height.

b. Cause: Damage to the RFID Antenna/Module.

Solution: Replace RFID Antenna/Module.

13.2.3 Symptom: Data Read Error

a. Cause: Failed or weak RFID tag.

Solution: Replace the RFID tag or manually assign the reagent.

13.2.4 Symptom: Reagent Registration warning

a. Cause: RFID Reader failed to update RFID tag information/RFID writing error.

Solution: Verify calibration. Replace or reprogram the RFID tag if it has failed to update (rare).

b. Cause: User removed the RFID tag from the rack before it could be updated during runtime.

Solution: Replace or reprogram the RFID tag.

13.2.5 Symptom: Cross-reading

a. Cause: RFID reader XYZ position is not calibrated.

Solution: Recalibrate RFID-R1.

b. Cause: RFID Reader position is too close to the RFID tags.

Solution: Position the 2D Barcode-RFID Bracket a little higher.

13.2.6 Symptom: Cannot connect to the RFID Reader

a. Cause: COM Port assignment changed or unavailable.

a. Solution: Restart the computer to recover the COM Ports. Reassign the COM Port
number.

b. Cause: RFID Reader connection issue.

MD-Stainer Service Manual V1._EN 85/173

 a. Solution: Verify that all pins on RFID Adapter A are securely seated in the connectors
on the RFID Module. Verify that the RFID Ribbon cable is undamaged and securely
seated and fastened in the connector on RFID Adapter A. Inspect the RFID Ribbon
cable for damage. Verify that the RFID Ribbon cable is securely seated and fastened
in the connector on RFID Adapter B.

c. Cause: Communications board failure.

a. Solution: Replace the Communications board.

d. Cause: 12-24V Power Converter failure.

a. Solution: Replace the 12-24V Power Converter.

e. Cause: RFID Module malfunctions.

a. Solution: Replace the RFID Module.

13.3 Maintenance/Repair: RFID Reader

1. Adjust the RFID Antenna Height

a. Unscrew the two captive screws and move the 2D Barcode-RFID Bracket up/down
within the slotted hole until it is in the desired position. Start by positioning the RFID
antenna at the lowest position.

b. Recalibrate RFID-R1.

c. Test RFID Reader consistency by testing a reagent rack of 40 RFID tags.

d. Adjust the reader height again if necessary.

2. Remove the RFID Cover

a. Unscrew the 2 hex nuts securing the top of the RFID Cover.

b. Unclip the RFID Cover.

3. Replace the RFID Antenna

MD-Stainer Service Manual V1._EN 86/173

 a. Unscrew the RFID Antenna cable from the port on the RFID Module.

b. Unscrew all 3 cable clamps securing the RFID Antenna cable to the Y arm.

c. Unwind the RFID Antenna from the 2D Barcode cable.

d. Unscrew the two captive screws to remove the 2D Barcode-RFID Bracket from the Y
arm.

e. Unscrew the 2 cable clamps securing the RFID Antenna cable to the bracket.

f. Remove the RFID Cover.

g. Remove the RFID Antenna from the 2D Barcode-RFID Bracket by unscrewing the 2 hex
nuts securing the top of the antenna and unscrewing the 2 hex nuts securing the
bottom of the antenna with the 2 pan-head screws securing the base.

h. Replace with a new RFID Antenna and secure with all screws and clamps.

i. Rewind the RFID Antenna cable around the 2D Barcode cable and through the bracket.
Verify that the cable does not interfere with the motion of the YZZ axes.

j. Ensure that the antenna is not crooked and positioned parallel to the XY plane. Gently
bend the bracket to bring it into position if necessary.

k. Reinstall the RFID Cover.

4. Replace the RFID Module

MD-Stainer Service Manual V1._EN 87/173

 a. Remove the Left Panel to access the module located on the YZZ assembly of the robot.

b. Unscrew the RFID Antenna cable from the module port.

c. Unscrew the 4 screws securing the module to the robot.

d. Detach RFID Adapter A from the module by loosening the screws on the 5 pin and 2
pin connectors.

e. Attach RFID Adapter A to the new RFID Module. Ensure that all pins line up.

f. Install the new module onto the robot.

g. Ensure that the ribbon cable is still securely fastened to RFID Adapter A.

h. Test RFID function before replacing the Left Panel.

5. Replace the RFID Adapter A

a. Remove Left Panel to access the adapter located on the YZZ assembly of the robot.

b. Loosen the screws on the 5 and 2 pin connectors that secure Adapter A to the RFID
Module.

c. Detach the RFID Ribbon cable by unclipping the fastener.

d. Fasten the Ribbon cable to the new RFID adapter A.

e. Install the new adapter onto the RFID Module.

6. Replace the RFID Adapter B

a. Refer to 18.4. Other Electronic Boards Replacement.

MD-Stainer Service Manual V1._EN 88/173

 b. Barcode Reader

13.4 Overview of 2D Barcode Reader Components

Part No. Description Quantit Function Image
y

PAT- PC325A 2D Barcode Cable A 1 USB Serial converter

cable

PAT- PC325B 2D Barcode Cable B 1 Serial cable

PAT- PC329 2D Barcode Reader 1 Reads 2D barcode labels

13.5 Troubleshooting: Barcode Reader

13.5.1 Symptom: Barcode Reader is not reading any slide positions.

a. Cause: Barcode Port is not connected.

Solution: Verify that the USB is connected to the designated port on the computer. Restart
the computer.

b. Cause: Barcode Reader is not calibrated.

Solution: Verify the Barcode reader XY position.

c. Cause: Barcode Reader is not tuned.

Solution: Move barcode reader to slot #1 and place a barcode label on the slide. Select Reader
Channel “1” and click “Tune Channel”.

13.5.2 Symptom: Barcode Reader is not reading certain slide positions.

a. Cause: Barcode Reader is not calibrated.

Solution: Verify the Barcode reader XY position.

b. Cause: Barcode Reader is not tuned.

Solution: Move barcode reader to slot #1 and place a barcode label on the slide. Select Reader
Channel “1” and click “Tune Channel”.

MD-Stainer Service Manual V1._EN 89/173

 c. Cause: Overhead lighting is interfering with the laser reading.

Solution: Close the instrument door. Move the instrument away from the overhead light.

d. Cause: Barcode Reader is not properly installed on the RFID-2D Barcode bracket. Cannot
physically move to the last row.

Solution: Adjust the barcode reader so that it sits at a 45 degree angle to the XY Plane.

13.5.3 Symptom: Cannot connect to the Barcode Reader.

a. Cause: COM Port assignment changed or unavailable.

Solution: Restart the computer to recover the COM Ports. Reassign the COM Port number.

b. Cause: Barcode Reader connection issue.

Solution: Verify the serial cable connection and USB converter cable connection to
Communications board.

c. Cause: Communications board failure.

Solution: Replace the Communications board.

d. Cause: Barcode Reader malfunctions.

Solution: Replace Barcode Reader.

13.6 Maintenance/Repair: Barcode Reader

1. Clean the Barcode Reader

a. Gently brush or blow away dust that may interfere with the camera/laser reader

2. Replace the Barcode Reader

a. Remove the X Cover in front of the robot to access the barcode cable.

NOTE: The 12V-24V converter/RFID adapter B boards block direct

access to the cable.

b. Remove the Back panel.

c. Unplug the converter cable from the communications board.

d. Unlock the brackets on the cable carrier using a narrow, rigid tool i.e.: screwdriver or
pen.

i. Hold the carrier slightly behind the area to be unlocked.

MD-Stainer Service Manual V1._EN 90/173

 ii. Insert the tool and pull up slightly. The brackets should unlock easily.

iii. Continue until the cable carrier is completely unlocked.

e. Remove the barcode reader from the bracket.

f. Remove the tape and clamps securing the bracket.

g. Replace with a new barcode reader.

h. Make sure it is installed at a 45 degree angle to the XY Plane.

i. Recalibrate Barcode-SP1.

j. Tune the barcode reader (with the shell on).

k. Verify the barcode reader on positions #1, #12, #25, and #36.

l. (Optional) Verify the barcode reader on all 36 slide positions.

MD-Stainer Service Manual V1._EN 91/173

 14 Hydraulics System (Pumps, Tubing and Probes)
14.1 Overview of the Tubing System Components
Part No. Description Quantity Function Image

PAT-PC410 Flangeless nut 5 Adapts tubing to

valve

PAT-PC404 Flangeless ferrule 8 Adapts tubing to

valve

PAT-PC412 1/8"OD PFA 4.5in (Pump1) Tubing to Y connector N/A

tubing
4.5in (Pump2) Tubing to Y connector N/A

9 or 15in (buffer Tubing to Y connector N/A

bottle)

PAT-PC418 1/8"OD PTFE 8.5ft (Z1-Pump1) Holds Reagent N/A

Tubing
9ft (Z2-Pump2) Holds Waste N/A

PAT-PC402 Y connector 1 Connects tubing

between Pump1,
Pump2 and buffer
bottle

PAT-PC408 Elbow insert 1 Adapts tubing in

buffer bottle

PAT-PC406 4x3x3mm FEP 7.5in Connects between Y N/A

tubing connector and female
fitting

PAT-PC407 Female fitting 1 Connects elbow

insert on buffer
bottle

PAT-PC070 Probe 2 Inserts on Z1/Z2

tubing

MD-Stainer Service Manual V1._EN 92/173

 14.2 Troubleshooting: Tubing

14.2.1 Symptom: Liquid is leaking from the probe collet.

a. Cause: The probe has detached from the tubing.

Solution: Inspect the tubing for crimping/damage. Cut the deformed piece of tubing where it is
attached to the probe and reinsert the probe. Replace the probe and/or tubing.

14.2.2 Symptom: The probe is rusty.

a. Cause: Protective Teflon coating is damaged or worn.

Solution: Replace the probe.

14.2.3 Symptom: A large number of bubbles appear in the tubing line after system
initialization. Liquid dispensation/aspiration is not reliable and is affecting staining
quality.
a. Cause: Tubing may be clogged, crimped, or leaking.

Solution: Inspect tubing. Perform the tubing cleaning procedure. Replace the probe and/or tubing.

b. Cause: A pump may be malfunctioning or leaking.

Solution: Replace the pump.

c. Cause: The insert on the buffer cap or the fitting on the tubing is damaged.

Solution: Replace the buffer bottle or female fitting on the tubing.

14.3 Maintenance: Tubing

14.3.1 Tubing Cleaning

The Z1 and Z2 (waste) tubing may slowly build up wax, DAB precipitate and other residues over time.
Tubing should be cleaned every 6 months (operating at 1 cycle a day) or 150 cycles of staining.

1. Prepare Tubing Cleaning Solution(s).

a. Fill two 15mL vials with the appropriate cleaning solution:

i. (Recommended) Use Bleach to remove DAB precipitate.

ii. (Recommended) Use Slide Brite to remove wax residues.

MD-Stainer Service Manual V1._EN 93/173

 b. Alternatively, use the Tubing Clean Kit.

2. Use the Tubing Clean feature in the System Utilities

a. Verify there is sufficient Wash Buffer in the wash bottle.

3. Login to the main user interface and open System Utilities > Tools.

4. Click “Tubing Clean”.

5. Load the reagents onto the specially-modified reagent rack (temporary) and mount the rack onto
the instrument.

a. Place Z1 tube cleaning solution on reagent rack position #1.

b. Place Z2 tube cleaning solution on reagent rack position #5.

6. Click “OK” to initiate the tube cleaning sequence. The Z1 and Z2 probes will both aspirate 5mL of
cleaning solution into the tubing from their respective reagent rack positions. The system will then
initiate a 20 minute countdown.

7. After 20 minutes has elapsed, the system will automatically perform a system initialization and
purge the cleaning solution waste. The user may click “Cancel” at any moment to immediately
purge the waste from the tubing.

8. Inspect the tubing. There should be no visible wax residues, DAB precipitate or salt build-up.

9. Repeat the Tube Cleaning function as needed.

14.3.2 Tubing Replacement

Tubing must be periodically replaced due to physical damage or strong build-up of waste/reagent
residues.

1. Clear the Tubing Lines

a. Unscrew the cap from the Wash Buffer Bottle, leaving it connected to the instrument.

b. Perform System Initialization two times to clear the line of buffer.

2. Remove the Z1/Z2 Probes

a. Unscrew the collet caps on the Z1 and Z2 axes.

MD-Stainer Service Manual V1._EN 94/173

 b. Gently pull the tubing down through the opening with a pair of rubber-tipped pliers. Be
careful not to scratch or bend the probes.

NOTE: The probes are protected by a Teflon coating that is resistant to

chemicals. Damage to this coating will eventually result in rusting and will require
a replacement.

c. Remove the probes from the tubing for re-use. Wipe away any reagent residue around
the tip with an alcohol pad.

3. Disconnect the Tubing from the Pumps

a. Remove the Left Access cover.

b. Use the extender tool to disconnect the tubing from the pumps. Use a paper towel to
soak up any leaks.

c. Remove the flangeless nuts and ferrules for re-use.

d. Blot the ends of the tubing with a paper towel to absorb any residual moisture in the
tubing.

4. Remove the Old Tubing

a. Secure a cap/electrical tape to the end of the tubing to prevent moisture from leaking
onto electronic components.

b. Unscrew all tubing clamps and remove the two pieces of tape securing the tubing to Y
arm.

c. Cut the cable tie securing the loop of tubing on the Y arm.

d. Pull the tubing out along the air baffle, through the cable carrier and out through the
collet.

5. Install the New Tubing

a. Insert a probe into each length of new tubing. Twist the probe until it is fully inserted; it
should fit snugly.

b. Thread the Z1 tubing through the Z1 arm (front). Be very careful not to deform/crimp the
tubing.

MD-Stainer Service Manual V1._EN 95/173

 c. Thread the Z2 tubing through the Z2 arm (back). Be very careful not to deform/crimp the
tubing.

d. Secure a cap/electrical tape at the end of the tubing to facilitate installation.

e. Secure the tubing to the Y arm with the tubing clamps. Be careful to control the length of
free tubing. The tubing should move smoothly along the entire Y axis without shifting or
getting entangled.

f. Gently guide and position the tubing to minimize contact with the housing, robotic arm
and cables.

g. Make a loop around the front right standoff of the controller board assembly on the Y
arm and thread the tubing through the cable carrier alongside the 2D barcode reader
cable. Secure with a cable tie.

h. Move the YZZ arm to the right side of the instrument to keep the cable carrier relatively
horizontal.

i. Continue threading the tubing through the cable carrier. Press down on the tubing
through the openings in the cable carrier if the tubing gets stuck.

j. Once the tubing has reached about halfway through the cable carrier, move the YZZ arm
to the left side of the instrument to keep the remaining length of cable carrier horizontal.

k. Thread the tubing through the hard nylon tubing through the opening on the X Cover.

l. Continue pushing the tubing through the air baffle on the back side of the instrument and
out through the top-right opening on the left mount.

MD-Stainer Service Manual V1._EN 96/173

 m. Re-tape the tubing if necessary and reinstall the collet caps.

6. Connect the Tubing to the Pumps

a. Remove the tape securing the ends of the tubing.

b. Install the flangeless nut and ferrule on the end of each length of tubing as shown.

c. Use the extender tool to connect the tubing to the pumps through the left mount as
marked. Do not over-tighten the nuts as this may cause the tubing to deform.

7. Verify Pump Function. Verify that the tubing is properly connected after reconnecting the pumps.

a. Connect the Wash Buffer Bottle to the instrument

b. Open the main user interface and click System Utilities > Tools.

c. Click Prime Pump1 to verify Pump 1 function. Repeat as needed.

d. Click Prime Pump2 to verify Pump 2 function. Repeat as needed.

8. Verify XYZ Calibration. Verify the calibration of the Z1 and Z2 probes after replacing the tubing.

a. Verify SP1-Z1 at module position #1. Bend the probe to re-center XY.

b. Verify XY Adjust-Z1 and SP-Z1. Recalibrate Z if needed.

MD-Stainer Service Manual V1._EN 97/173

 c. Verify SP1-Z2 at module position#1. Bend the probe to re-center XY.

d. Verify XY Adjust-Z2 and SP-Z2. Recalibrate Z if needed.

14.4 Overview of Pump Components

Part No. Description Quantity Function Image

PC703 Pump, 5mL 1 (Pump1) Dispenses reagents

1 (Pump2) Extracts waste

PC332/PC702 Cable-Pump Interface 1 Connects pump controller boards N/A

to Interconnect

14.5 Troubleshooting: Pumps

14.5.1 Symptom: Pump is producing abnormal noises or fails to initialize.

a. Cause: Reagent waste residues or wax cause a blockage in the Z2 tubing.

Solution: Perform the tubing cleaning procedure or replace the tubing.

b. Cause: Intermittent cable connection.

Solution: Inspect the controller board on the pump for a loose cable connection and
inspect all connectors for good contacts.

c. Cause: Damaged Cable Pump Interface. May generate a timeout or initialization error.

Solution: Inspect the wires for good contact to the crimp terminals. Replace the Cable
Pump Interface.

d. Cause: Malfunction of the electronic parts/PCB on pump.

Solution: Replace the pump. Please contact Vitro for further technical support.

14.5.2 Symptom: Pump produces a “clack” sound at every draw/dispense.

a. Cause: Valve defect.

Solution: Replace the pump if problem persists.

MD-Stainer Service Manual V1._EN 98/173

 14.5.3 Symptom: Pump plunger is stuck.
a. Cause: Motor malfunction due to liquid damage.

Solution: Replace the pump.

b. Cause: Intermittent cable connection.

Solution: Inspect the controller board on the pump for a loose cable connection and
inspect all connectors for good contacts.

14.5.4 Symptom: An extensive salt crust (may be discoloured) has built up around the syringe
and/or motor.
a. Cause: Syringe seal is damaged.

Solution: Replace the pump.

14.5.5 Symptom: Z1 and/or Z2 pump does not respond.

a. Cause: Intermittent cable connection.

Solution: Inspect the controller board on the pump for a loose cable connection and
inspect all connectors for good contacts. Verify the connection of the 12-24V Power
Converter cable to the Interconnect PCB and the 12-24V Power Converter. Verify the
connection of the Cable Pump Interface to the pumps and the Interconnect PCB.

b. Cause: Damaged Cable Pump Interface. May generate a timeout or initialization error.

Solution: Inspect the wires for good contact to the crimp terminals. Replace the Cable
Pump Interface.

c. Cause: Interconnect PCB failure. May generate a timeout error.

Solution: Consult Vitro Technical Support. Replace the Interconnect PCB.

MD-Stainer Service Manual V1._EN 99/173

 14.6 Maintenance: Pumps
The pumps can be accessed by removing the Back panel of the outer housing. Perform regular
inspections and routine cleaning to prevent damage to the syringe or plunger.

14.6.1 Pump Cleaning

It is normal to see white salt residue build up around the pump syringe overtime.

a. Salt flakes will accumulate around the syringe and step motor due to buffer
evaporation. They can be carefully vacuumed or brushed away. Remove all salt flakes
around the electronic components.

b. Large salt crystals or other residues may gradually build up around the pump syringe
and step motor shaft. This may require removal of the pump for more thorough
cleaning with water or alcohol. Be very careful not to drip water onto the exposed
electrical components. Also be careful not to scratch or damage the syringe while
cleaning.

c. After removing the pumps, hold the pump with the electronic boards facing up.

d. Use a damp cotton swab to wipe away the salt. Use a pipette to carefully add a few
drops of liquid to dissolve the salt crust as needed. Slowly twist the motor shaft to
dislodge the salt. Wipe away the salt and liquid.

e. Yellow/discoloured salt crystals or an obvious trail of salt down the valves, pump
syringe or step motor shaft may indicate a pump seal leakage. This will require a pump
replacement.

14.6.2 Pump Replacement

The pump may need to be replaced if it is a) presenting with repeated errors/warnings, b) dispensing
inaccurate/inconsistent reagent volumes or c) leaking from the valves or plunger seal.

1. Remove the Pump-Bracket Assembly. The pumps are installed on a pump bracket for easy
removal.

a. Unscrew the cap from the Wash Buffer Bottle, leaving it connected to the instrument.

b. Perform System Initialization two times to clear the line of buffer.

c. Remove the Left Access cover.

d. Use the extender tool to disconnect the tubing (2 lines IN, 2 lines OUT) from the
pumps. Avoid spilling liquid onto the exposed electronic components. Use a paper
towel to soak up any leaks from the tubing or the valves.

MD-Stainer Service Manual V1._EN 100/173

 e. Carefully disconnect the cable pump interface from the pumps. Do not pull directly
on the wires as it may damage the contacts on the crimp terminals.

f. Unscrew the pump bracket from the left mount and carefully remove the entire
pump-bracket assembly.

g. Perform cleaning/maintenance on the pumps if needed.

2. Replace the Pump on the Pump-Bracket Assembly

a. After removing the pump-bracket assembly from the system, disconnect the cable
pump interface from the malfunctioning pump.

b. Unscrew the pump from the bracket and replace with a new pump.

Address Switch

(set to 1 or 2)

3. Set the Address Switch on the Pump. Use a small flat head screwdriver to set the address
switch (should feel a slight catch or click when it is in position).

MD-Stainer Service Manual V1._EN 101/173

 a. The Z1 pump (inside of the instrument) is set to address 1.

b. The Z2 pump (backside of the instrument) is set to address 2.

4. Reinstall the Pump-Bracket Assembly

a. Inspect the crimp terminals on the cable pump interface. Verify that the wires are fully
seated in the connector.

b. Reconnect the cable pump interface to the pumps.

c. Mount the pump-bracket assembly back onto the system.

d. Ensure that the motor shaft on both pumps is properly aligned with the corresponding
hole on the pump shaft cover (located on the bottom side of the equipment pan).
Otherwise, misalignment will create interference during pump operation and may
result in severe damage.

e. Verify the pump function after reconnecting the pumps.

MD-Stainer Service Manual V1._EN 102/173

 15 Calibration Instructions
15.1 Module Calibration

15.1.1 Connect to the Slides

1. Open the PathCom Autostainer Server > Slides > General tab.
2. Connect to the Slides Terminal.

3. Accessing the Slides Calibration Interface. Click on Calibration tab.

MD-Stainer Service Manual V1._EN 103/173

 4. Select a module from the Module Positions panel on the left to access the Adjust panel.

15.1.2 Overview of Group Commands

1. Group commands may be accessed from the Module Positions panel on the left side.
a. Click the “Home” button to lift all 36 module lids to the Home position.
b. Click the “Down” button to lift all 36 module lids to the Down position.
c. Click the “Extract” button to lift all 36 module lids to the Extract position.
d. Click the “Prime Z1” button to prime the Z1 pump.

NOTE: Make sure to Connect to the Robot Terminal and initialize the robot and pumps. Click
the “Prime Z2” button to prime the Z2 pump.

NOTE: Make sure to Connect to the Robot Terminal and Initialize the robot and pumps.

e. Click the “Inject Buffer” button to inject wash buffer into a selected group of
modules.

NOTE: Make sure to Connect to the Robot Terminal and Initialize the robot and pumps. Also,
make sure that the buffer bottle is connected to the system and the tubing line is primed.

2. Select the modules using the pop-up window and adjust the volume using the up/down
arrows. The system will automatically move the modules to the Extract position before injecting
buffer.

MD-Stainer Service Manual V1._EN 104/173

 a. Click the “Extract Buffer” button to extract wash buffer from a selected group of
modules.

NOTE: Make sure to Connect to the Robot Terminal and Initialize the robot and pumps. Also,
make sure that the buffer bottle is connected to the system and the tubing line is primed.

b. Select the modules using the pop-up window and adjust the volume using the
up/down arrows. The system will automatically move the modules to the Extract position
before injecting buffer.

3. Click “Backup All Modules” to save all current calibration values to the system data file
PathCom/PathCom Autostainer/Data/SlideProcData.xml

15.1.3 Overview of Module Commands

Module calibration values and commands may be accessed from the Adjust panel on the right side.

The system will load and display all current calibration values, device serial number, firmware version,
temperature offset and the current motor position for the selected module.

Click “Set/Go” to write the current Home position value to the module and move the lid to the
Home position. Click “Go” next to Down, Extract, Inject, or A1-A7 to move to the corresponding
position.

The calibration values may be adjusted by entering a new value or clicking the up-down arrows next
to the corresponding position. This method will not move the module lid.

MD-Stainer Service Manual V1._EN 105/173

 Alternatively, the calibration values may be adjusted by clicking the Lid Up and Lid Down arrows. This
method will move the module lid.

Click “Save All Parameters to Module” to write all current calibration values to the module.

Click “Restore Current Module” to load and write saved calibration values from the data file to the
current selected module.

15.1.4 Calibrate the Home position

1. Insert a standard 1mm slide and a calibration chamber onto the module.
a. Lift the module lid to Home then move the lid to Down.
b. Count the number of clicks that the motor overdrives.
i. If the number is > 5 clicks, increase the Home position value by (#clicks – 4) x
4 steps.
ii. If the number is < 3 clicks, decrease the Home position value by (4-#clicks) x
4 steps. Repeat this procedure until 3-5 clicks are heard.

15.1.5 Calibrate the Extract position.

1. With the slide still inserted, lift the module lid to Home then Down then Extract.
a. Place the 13.5mm height gauge on the slide in front of the module lid.
b. Move the lid up or down until the top of the module lid is level with the gauge.

15.1.6 Calibrate the A7 position.

1. With the slide still inserted, lift the module lid to Home, then go to Down then Extract. Inject
120uL wash buffer.
a. Move the lid to the A7 position.
b. The buffer should reach line 8 without filling the entire chamber.
c. Adjust the angle of the lid down if the buffer does not reach line 8.
d. Adjust the angle of the lid up if the buffer fills the entire chamber.

NOTE: If leaking is observed, or the chamber fails to fill up properly, clean and dry the slide
and start over.

MD-Stainer Service Manual V1._EN 106/173

 15.1.7 Calibrate the Inject position.
1. With the 120uL still filling the chamber, move the lid to the Inject position. The buffer should
reach mid-way to line 1.

15.1.8 Calibrate the A4 position.

1. Add an additional 80uL of wash buffer for a total of 200uL.
a. The buffer should reach line 8 without filling the entire chamber.

MD-Stainer Service Manual V1._EN 107/173

 15.1.9 Calibrate the A3 position.
1. Add an additional 200uL of wash buffer for a total of 400uL.
a. The buffer should reach line 8 without filling the entire chamber.

15.1.10 Calibrate the remaining agitation angles.

1. (Optional) Set the A1 position to 100.
2. (Optional) Set the A2 position. Estimate a value between 2-6 steps above A3.
3. (Optional) Set the A5 position. Estimate a value 1/3 between A4 and A7.
4. (Optional) Set the A6 position. Estimate a value 2/3 between A4 and A7.

15.2 Robot Calibration

1. Open the PathCom Autostainer Server > Robot > Setup tab.
2. Connect to the Robot Terminal and click Initialize to initialize the robot.
3. Next Click on Calibration Tab

MD-Stainer Service Manual V1._EN 108/173

 4. To perform calibration, select one of following options from the Calibrate dropdown menu.
5. Select a position from the display on the left to access the Adjust Position controls on the
right.

15.2.1 Default Depths

MD-Stainer Service Manual V1._EN 109/173

 Calibration is performed at a reference Z height for the majority of positions. The default depths are
the values that are added to the calibration reference height to obtain the actual Z height used during
runtime.

Default depths cannot be edited from the Calibration Interface. The user must directly edit depth
values in the MotorControlData.xml file under the <DefinedZDepth> if they require adjustment.

The file is located in C:/PathCom/PathComAutostainer/Data Close the Autostainer Server and re-
open it.

Click the Robot > Calibration tab and click “Save” in Default Depths to apply the changed depths to the
calibration values.

15.2.2 References (Not implement / For future use)

The reference position is set at a stable and fixed point on the deck plate that can be used to verify
that the probes/robot position have not been bent/drifted over time. A reference position pin will
be implemented on future deck plates. For each Z axis probe, position the Z axis directly over the
pin and save the coordinates.

MD-Stainer Service Manual V1._EN 110/173

 15.2.3 Wash and Waste Station
There is a standard waste station and hazardous waste station, each with 4 calibration positions:

Standard Wash Z1: Positioned over the deep wash hole for Z1 on the standard waste station.

Standard Wash Z2: Positioned over the shallow wash hole for Z2 on the standard waste station.

Standard Waste Z1: Positioned over the waste hole for Z1 on the waste station.

Standard Waste Z2: Positioned over the waste hole for Z2 on the waste station.

Hazardous Wash Z1: Positioned over the deep wash hole for Z1 on the hazardous waste station.

Hazardous Wash Z2: Positioned over the deep wash hole for Z1 on the hazardous waste station (select
the wash hole for Z2 on the figure).

Hazardous Waste Z1: Positioned over the waste hole for Z1 on the hazardous waste
station. Hazardous Waste Z2: Positioned over the waste hole for Z2 on the
hazardous waste station.

MD-Stainer Service Manual V1._EN 111/173

 Place the calibration tool on the wash/waste station and verify all 4 calibration positions for each
waste station. The probe should be centered directly over the pin on the calibration tool for each
position.

To test the deep wash function, remove the calibration tool, reconnect the wash buffer bottle, select
the wash position and click “Wash Test”. The robot and pumps will initialize and dispense 1200uL of
wash buffer into the selected position. The buffer should overflow and clean the exterior surface of
the probe.

NOTE: To implement the deep wash for Z2 on the hazardous waste station, the user must:
Copy/paste WashH-Z2.xml and CorrectionSets.xml to C:/PathCom/PathComAutostainer/Data

Set the spacing for the defined horizontal position WashH-Z2 to X Spacing = 1 and Y Spacing = 1 and
click “Accept Data Above” in the Robot/Set Positions tab then “Save Configuration” in the Robot/Setup
tab.

15.2.4 RFID Tag

Place a vial with an RFID tag on reagent rack position #1.

Move to the calibration position and place the calibration tool through the hole on the covered RFID
reader. It should be centered over the RFID tag.

Click “Test RFID Runtime position” to verify the actual runtime position for the RFID reader (-40 steps
from the calibration position).

MD-Stainer Service Manual V1._EN 112/173

 Test the reader function by using the RFID tab on the Autostainer Server or using the Scan Reagents
feature on the main user interface.

NOTE: To implement the RFID reader runtime position, the user must: Copy/paste RFID-
R1.xml to C:/PathCom/PathComAutostainer/PositionCorrectionData Each position for Y is set to -40
in the correction offset table.

15.2.5 Barcode
Insert a labelled slide and chamber onto module position #1.

Turn on the laser pointer on the Barcode reader by checking the box “Laser Pointer On”.

For SR-610, the upper laser point should be positioned on line 3 of the chamber. The lower laser point
should be aligned with the upper laser point.

For SR-710, the two converging laser points should be centered over the barcode label on the slide.
Tune and test the reader function by using the Barcode tab on the Autostainer Server.

MD-Stainer Service Manual V1._EN 113/173

 15.2.6 Reagent Vials
There are 40 reagent vial positions on the reagent rack.

Position #1 serves as a base coordinate while the remaining 39 positions are saved in a correction
offset table.

Place the calibration tool in the upper left corner position #1 and verify the calibration of Z1.

MD-Stainer Service Manual V1._EN 114/173

 The probe should be centered directly over the pin on the calibration tool.

Verify the remaining 3 corner position calibrations of Z1 using the tool. The calibration software will
automatically interpolate the remaining 36 coordinates on the reagent rack for Z1.

Select the upper left corner position #1 and verify the calibration of Z2. The probe should be centered
directly over the pin on the calibration tool.

Click “Copy Z1 Correction Table to Z2” to copy the correction offset table for Z1 to Z2.

15.2.7 Modules
There are 36 module positions on the slide deck.

There are two robotic probe positions for each module position: Z1 and Z2

Position #1 serves as a base coordinate while the remaining 36 positions are saved in a correction
offset table.

MD-Stainer Service Manual V1._EN 115/173

 Click “Lids Up” to raise all module lids.

Click “Lids Down” to lower all module lids.

Place the calibration tool in the upper left corner position #1 and verify the calibration of Z2. The probe
should be centered directly over the pin on the calibration tool.

Verify the remaining position calibrations of Z2 using the tool.

NOTE: Make sure to Home the robot after calibrating each row of 12 modules.

Select the upper left corner position #1 and verify the calibration of Z1. The probe should be centered
directly over the pin on the calibration tool.

Click “Copy Z2 Correction Table to Z1” to copy the correction offset table for Z1 to Z2.

MD-Stainer Service Manual V1._EN 116/173

 After completing calibration for all 36 modules using the calibration tool, insert a chamber and slide
into position #1 and verify the calibration of Z2. Adjust the Y coordinate 2-3 steps back for position #1.
The probe should be ~2 steps behind the center point of the chimney.

Repeat for Z1.

15.2.8 Home
At any time during calibration, the user may click “Home” to move the robot to the Home position (0,
0, 0) and re-initialize the robot twice.

15.2.9 Adjust Position Controls

Select a calibration position from the display on the left to access the Adjust Position controls on the
right.

MD-Stainer Service Manual V1._EN 117/173

 A set of coarse adjustment and fine adjustment arrows are used to adjust the calibration along
the three axes XYZ. The coarse adjustment step value may be set by the user.

The fine adjustment step value is set at 1.

Click “Save” to save the new calibration offsets for the current selected position.

Click “Verify” to save, go Home and move back to the current selected position to verify the new
calibration offsets of the current selected position.

Click “Next” to move the robot to the next coordinate on the display to continue calibration.

15.2.10 Apply Depth

Click “Apply Depth” on the Adjust Position controls to move the robot to the actual run time position
(after depth is applied).

The depth is displayed in the greyed-out box Depth:

IMPORTANT: ONLY USE THIS FEATURE WHEN THE CALIBRATION TOOLS ARE REMOVED! To
un-apply the Depth, click “Apply Depth” again.

15.2.11 Safe Mode

Check the box Use Safe Mode with Safety Steps: to begin calibration with an additional Z offset /
”Safety Steps” above the calibration position to avoid hitting the calibration tools with the probe. This
feature is available for all applicable positions with a Z coordinate value.

MD-Stainer Service Manual V1._EN 118/173

 Adjust the number of safety steps using the up/down arrows. The user may need to un-check and re-
check the box to apply the change.

Use the coarse and fine adjustment tools for XYZ to adjust the calibration.

Click “Save” to save the current position coordinates and offsets (if applicable).

Click “Verify” to save and verify the current position coordinates. The Safety Steps will no
longer be applied. Click “Next” to move to the next position.

After completing calibration, uncheck the box for Use Safety Mode... in order to re-verify all calibrated
positions without Safety Steps applied.

15.2.12 Show Coordinate (for advanced users only)

Check the box Show Coordinate to display the base coordinates, offsets and current coordinates for
the current selected position. The user may use this feature to directly adjust the XYZ offsets in the
correction table.

MD-Stainer Service Manual V1._EN 119/173

 16 Computer
16.1 Setup a New Computer

16.1.1 System Requirements

a. English-based 64 bits Microsoft Windows 7 with the following or better configuration:

i. Intel Core i5-2410M CPU 2.3 GHz

ii. 4 GB RAM

iii. 500 GB Hard Drive

iv. 4 USB 2.0 communications ports

v. 1366 x 768 Screen Resolution

16.1.2 Setting Up a New Computer

a. Disable Windows power management, screen saver/display settings, auto update,
auto time synchronization, auto disc-scan, wireless internet connection, etc. features

i. Any of the above applications may interrupt the staining process if run during
the staining operation period.

ii. Disable the Windows Update Service

b. Set the computer name to the instrument serial number, i.e.: PC12017, or PC13055
etc.

c. Set the computer admin user name to: PathCom

d. Set computer admin user password to: PathCom

e. Copy the new PC files folder to the Local Disk C:\; this folder contains all drivers and
programs for setting up a new computer for the MD-Stainer Slide Stainer.

16.1.3 Copying the PCStainer Software to a New Computer

a. Copy the original C:\PathCom folder to the Local Disk C:\ on the new computer.

b. Install the latest version of the PCStainer Software.

i. Open the latest Installer Package.

ii. Click “UninstallPathCom.vbs” and follow the installation instructions.

iii. Click “InstallPathCom.vbs” and follow the installation instructions.

MD-Stainer Service Manual V1._EN 120/173

 NOTE: To install the PCStainer Software, see Software and Firmware Upgrade Guideline.

16.1.4 Additional Windows Applications and Drivers

1. Installing Fonts

a. Open C:\new PC files\Fonts\...

i. Open and install WINGDNG2.TTF

ii. Open and install WINGDNG3.TTF

b. Do not install andale32.exe and not restart the computer

1. Installing FTDI Drivers

a. Open C:\new PC files\FTDI Driver\...

b. Run twice CDM2.04.06.exe and follow installation instructions.

2. Installing the Visual Basic Power Pack

a. Open C:\new PC files\FW\...

i. Run and follow installation instructions.

3. Installing the QED Actuator Update Utility

a. Select Folder Actuator V3003 Update Utility > Publish > Setup > install > comport > Ok
or esc.

4. Installing Communication Board Update Utility

a. Open C:\new PC Files\FW\Comm_Board_update…\publish\…

i. Run setup.exe and follow the installation instructions.

1. Select the COM Port# when prompted.

5. (Optional) Installing NotePad++ to read logs and data files

a. Open C:\new PC files\NotePad++\...

16.1.5 PCStainer COM Port Assignment

1. Connect the instrument to the designated USB port on the computer, and power the
instrument on.

MD-Stainer Service Manual V1._EN 121/173

 a. Please maintain a dedicated USB port for the instrument, as connecting to a new port
may cause the COM Port assignment to change.

2. Go to Device Manager

a. USB-Serial Converter > right click > update driver software > browse my computer >
let me pick from a list > Universal Serial Bus > Have Disk > Browse > Computer >
Windows C : > New PC Files > Keyence Converter Cable > Keyence FTDI Drivers > FTDI
Bus > Ok > Next > Yes > Install this driver software anyway > Close

b. USB Serial Port > right click > update driver > Browse my computer > let me pick > Port
(COM and LPT) > have disk > browse > FTDI Port > Ok > Next > Yes > Install driver
software anyway > Windows has successfully installed > Close

3. The Com6 installed correctly displayed.

16.1.6 Setting the device SNR of the slide module Processor

1. Launch and display the AutoStainer Server UI

a. c:\PathCom\PathCom Autostainer\PathComAutoStainer.exe.

2. You can find three new applications at the Windows Toolbar, click on right click on the
SlideProcessor Application.

a. Select SlideTerm

b. Click on the Settings button

MD-Stainer Service Manual V1._EN 122/173

 3. Copy the first identifier of the DeviceSNR Combo box.

MD-Stainer Service Manual V1._EN 123/173

 4. Open and edit C:\PathCom\PathComAutoStainer\Data\SlideProcTermSettings.xml with
Notepad++

a. Paste a different Device SNR into the file i.e.: <port> RMQ1TAZ5 </port>

5. Close the Autostainer Server UI and save the file.

6. Re-launch the server and select the “Slides” tab.

a. Click Connect to connect to the slide module processor.

NOTE: If the connection is not successful, an error message will be displayed such as
“Port Unavailable”.

7. Test the Slides connection.

a. Select the checkbox Broadcast or input a specific Device Address (1st row: 1-12; 2nd
row: 13-24; 3rd row: 25-36).

b. Select “Home” from Move To Fixed Position, and click “Go”. The selected slides will
go to the Home position.

c. Select “Down”, and click “Go”. The selected slides will go to the Down position.

8. Repeat with a different Device SNR until the slide module processor is successfully connected.

16.1.7 Setting the device SNR of the robot (xyzz system and pumps)

1. Launch and display the AutoStainer Server UI

a. c:\PathCom\PathCom Autostainer\PathComAutoStainer.exe.

2. You can find three new applications at the Windows Toolbar, click on right click on the
SlideProcessor Application.

a. Select RobotTerm

MD-Stainer Service Manual V1._EN 124/173

 b. Click on the Settings button

3. Copy the first identifier of the DeviceSNR Combo box.

4. Open and edit C:\PathCom\PathComAutoStainer\Data\RSPSettings.xml with Notepad++

MD-Stainer Service Manual V1._EN 125/173

 5. Paste the Device SNR into the file i.e.: <port> RMQ1TA25 </port>

6. Close the Autostainer Server UI and save the file.

7. Re-launch the server and select the “Robot” tab.

a. Click Connect to connect to the robot

NOTE: If the connection is not successful, an error message will be displayed such as
“Port Unavailable”.

8. Test the Robot connection.

9. Click Initialize. The XYZZ robot and pumps should home and initialize.

10. Repeat with a different Device SNR until the robot is successfully connected and initialized.

16.1.8 Setting the RFID Reader COM Port#

1. Verify that the instrument is powered on and connected to the computer.

2. To launch the AutoStainer Server UI, open C:/PathCom/PathComAutoStainer

a. Run PathComAutostainer.exe

b. Click “OK” to close any pop-up messages, then click the icon on the Windows
task bar to display the Server UI

3. Select the RFID tab

MD-Stainer Service Manual V1._EN 126/173

 a. Change the Com Port Number to one of the port numbers found in the Device
Manager (i.e.: 3, 4, 5 or 6)

i. Click the check box Port Connected to connect to the RFID reader.

NOTE: If the connection is not successful, an error message will be displayed

such as “Reader not found or not ready”

ii. Continue trying new port numbers until the RFID reader is successfully
connected.

b. Test the RFID Reader function

i. Click the check box Reader Power On

ii. Place an RFID tag underneath the antenna and click Read RFID

iii. A 16-digit ID i.e.: “E0237492063E065D” will be read and displayed to the right.

iv. Note: The checkbox ISO15693 should also be checked to enable RFID writing.

MD-Stainer Service Manual V1._EN 127/173

 c. Open and edit C:\PathCom\PathComASGui\Data\TagSysRfidData.XML with
Notepad++

i. This file configures the COM Port for the RFID TagEditor.

ii. Set the port number to be the same number as determined above i.e.:
<ComPortNum>3</ComPortNum>

iii. Save the file.

16.1.9 Setting the 2D Barcode Reader COM Port#

1. Verify that the instrument is powered on and connected to the computer.

2. Launch and display the AutoStainer Server UI

3. Select the Barcode tab:

a. Click Com Setup and change the port number to one of COM Port Numbers (3,4,5,6)
found in the Device Manager above: i.e. COM6 and click “OK.

i. Click the checkbox Use Port Name to connect to the barcode reader.

ii. Continue trying new port numbers until the Barcode reader is successfully
connected.

b. Test the Barcode Reader function.

i. If the barcode reader is successfully connected, the functions to the left will
be enabled, and the Last Status will change from “Unknown” to “Present”.

ii. Check and uncheck Laser Pointer On to verify the position of the two laser
pointers underneath the 2D Barcode reader.

16.2 Setup Network

16.2.1 System Requirements

Windows 7

a. Default Windows (Admin) User Name: PathCom

b. Default Windows (Admin) Password: PathCom

c. The user may change the User Name and Password at Control Panel/User Accounts

Computer Name

MD-Stainer Service Manual V1._EN 128/173

 a. All Computer Names on the MD-Stainer Home Network must be unique.

b. The default Computer Name is set to the instrument serial number i.e.: PC11007.

c. The user may change the computer name under Computer > System Properties

i. Open Windows Explorer and select Computer.

ii. Right-click and select Properties.

iii. Open Advanced system settings from the panel on the left.

iv. Open the Computer Name tab and click Change… to rename the computer.

v. Restart the computer after changing the computer name.

Hardware Requirements

a. Network Switch (usually with one input port and 4 output ports)

b. Internet Cables (must be long enough to connect the Network Switch to the MD-Stainer
system)

c. Connect the MD-STAINER computers to the Internet Router:

i. Connect the Internet Cable from Line 1 on the router to one of the MD-Stainer
computers. The user may set the first MD-Stainer computer as the network
server.

ii. Connect the Internet Cable from Line 2 on the Switch to the 2nd MD-Stainer
computer.

iii. Repeat for the 3rd, 4th etc. MD-Stainer computer.

16.2.2 Home Network Settings

1. Turn off the laptop wireless connection using the Wi-Fi on/off button.

2. Setup the first MD-Stainer computer as the MD-Stainer Home Network Server.

a. Go to Control Panel > Network and Internet and click “Create a home group”.

NOTE: This may appear different on different computer models or versions of

Windows.

MD-Stainer Service Manual V1._EN 129/173

 b. Set/change the computer’s network location to the Home network.

c. Select to share Printers only.

d. Setup the Home network password.

i. When a Home network is created, a random password will be assigned, i.e.:

1Pr9ET5bJ5.

MD-Stainer Service Manual V1._EN 130/173

 ii. If there is already an existing Home Group, click “Leave home group”, then re-
join the new Home Group.

iii. Under Control Panel > Network and Internet > Home Group, click Change the
password…

e. Share the network directory at C:/PathCom/PathComASGui/Network.

i. Right-click the folder and select Sharing (read and write).

16.2.3 Shared Printer Settings

1. Connect the label printer to the MD-Stainer Home Network Server.

2. Login to the main user interface to test the label printing function.

3. Verify the printer name under System Utilities > Settings > 2D Barcode Format.

4. Share the barcode label printer (Z-Designer TLP 3844-Z or GX430t).

a. Open Control Panel > Hardware and Sound > Devices and Printers.

b. Right-click on the printer device icon and select Printer Properties.

c. Select the Sharing tab, and check the box Share this printer.

NOTE: Share only one printer at a time. Sharing more than one printer may cause unexpected
problems.

16.2.4 Join the MD-Stainer Home Network

6. Connect the second computer to the MD-Stainer Home network.

a. Open Control Panel > Network and Internet > Home Group

b. Click “Join Now” and follow the instructions to join the MD-Stainer Home network

MD-Stainer Service Manual V1._EN 131/173

 i. Enter the MD-Stainer Home network password, i.e.: PathCom11007.

c. Share the network directory at C:/PathCom/PathComASGui/Network.

7. Repeat to connect the remaining MD-Stainer computers to the Home network.

16.2.5 Configure the PCStainer Software to the MD-Stainer Home Network

1. Connect all MD-Stainer systems to the Home network.

2. Using the first computer, login to the main user interface.

3. Connect to other MD-Stainer systems on the network.

a. Click “Find All Network Machines” under System Utilities > Network

b. All computers on the Home network will be displayed under Available Network
Machines.

c. Select an MD-Stainer computer from the list and click “Select”.

d. Enter the User ID and Password (use the Windows User login).

i. Windows Default User Name: PathCom

MD-Stainer Service Manual V1._EN 132/173

 ii. Windows Default Password(case-sensitive): 6747l

4. The MD-Stainer computer will be displayed under Selected Network Machines when the
system has successfully established a connection.

a. Click “Test Connection” to verify the network connection.

5. Repeat. Connect to all available MD-Stainer computers on the network.

6. Click “Remove” to remove a computer from the list of Selected Network Machines.

a. The user should remove any computer that is no longer connected to the Home
network from the list of Selected Network Machines.

7. Link all MD-Stainer systems together on the network.

a. Repeat the procedure above for the remaining MD-Stainer computers.

16.2.6 Configure the MD-Stainer Computer to use the Shared Printer

2. Set the Shared Printer as the designated printer for all MD-Stainer systems on the network.

3. Open Control Panel > Hardware and Sound > Devices and Printers.

a. Click Add a printer.

b. Select Add a network printer.

c. Select the Shared Printer (it should be connected to the computer serving as the MD-
Stainer Home Network Server).

4. Login to the main user interface.

a. Open System Utilities > Utilities > Settings > 2D Barcode Format and select the Shared
Printer from the dropdown menu Printer:

b. i.e.: //PC11007/ZDesigner TLP 3844-Z

MD-Stainer Service Manual V1._EN 133/173

 5. Repeat for remaining MD-Stainer computers.

16.2.7 Test the MD-Stainer Home Network for LIM/LIS Sharing and Label Printing
2. Login to the main user interface on each MD-Stainer computer.

a. Prepare and print several barcode labels using the Shared Printer.

b. Interchange the labels across different MD-Stainer systems.

c. Scan Slides to read the labels.

3. Barcode labels that were prepared and printed from different MD-Stainer computers will be
recognized by any MD-Stainer system on the Home network.

MD-Stainer Service Manual V1._EN 134/173

 16.3 Setup LIS
The HL7 Server must be connected on a network to the MD-Stainer Computer.

16.3.1 Setup HL7 Server

1. Obtain the IP Address and Port Number from the MD-Stainer Computer.

a. The IP Address can be obtained by opening the Command Prompt window and
entering “ipconfig” into the prompt. Scroll to find the address i.e.: IPv4 Address
10.0.0.9

b. The Port Number is always set to 6759 (fixed by the software).

16.3.2 Setup Computer

2. Obtain the IP Address and Port Number from the HL7 Server.

3. Open the MD-Stainer main user interface.

4. Open System Utilities > LIM and check the box HL7 Connection Enabled.

MD-Stainer Service Manual V1._EN 135/173

 5. Input the HL7 Server IP Address and HL7 Server Port Number into the available fields.

6. Check the box Send Result When Finished.

7. Enter the Connector Application Name: “HL7 Connector”.

8. Click “Save Settings” and “Return”.

9. Exit the MD-Stainer main user interface.

16.3.3 Open the HL7 connector application.

1. Log back into the MD-Stainer main user interface. The HL7 Connecter application will
automatically open.

MD-Stainer Service Manual V1._EN 136/173

 16.3.4 Test the connection.
1. Edit the HL7TestMsg.txt file located in PathCom/PathComASGui/Data

MSH|^~\&|LISServer|Hops.Name1|YouIHCInstrument|Hosp.Name2|201112071154||OML^O21|
20111207115404765355942B11-13962A|T|2.4
PID|1|355924|455924||SURNAME1^SURNAME2^SURNAME3|||M|
PV1|1||||||CODEDOCTOR1^DOCTOR1^JUAN|CODEDOCTOR2^DOCTOR2^PEDRO|CODEDOCTOR3
^DOCTOR3^MARIA||||||||CODEDOCTOR4^DOCTOR4^CRISTINA
SPM|1|A||TISSUECODE^TISSUEDESCRIPTION||||||
SAC|B11-13926-A-|B11-13926-A|A-1
ORC|NW|B11-13962
OBR||483003||CALDESM|||201112071154||||||||||||

2. Change the date to within 3 months of the current date.

3. Click “Test” in the HL7 Connector application to test the connection between the MD-Stainer
computer and the HL7 server.

4. Alternatively, create a message in the available message box in the HL7 Connector application.
Click “Send” to test the connection between the MD-Stainer computer and the HL7 Server.

16.3.5 Access HL7 logs

To access the HL7 message logs, go to C:/PathCom/PathComASGui/Logs/HL7

MD-Stainer Service Manual V1._EN 137/173

 16.4 Installing the Zebra Label Printer (currently compatible with models Zebra
TLP3844-Z, GX430t)

16.4.1 Setting Up the Zebra Printer

1. Follow the manufacturer’s instructions for installing the label roll and media ribbon if
necessary.

16.4.2 Installing the Zebra Setup Utilities and Printer Driver

1. Connect the printer to the designated USB port on the computer. Keep it powered off for now.

2. Please maintain a dedicated USB port for the label printer.

3. For model TLP3844, open C:\new PC files\Zebra TPL3844-Z Driver\ Zebra_ZPLII_Utility\ …

4. Run the setup application ZSU_114838.exe and follow the installation instructions.

5. For model GXT430t at C:\new PC files\Zebra GXT430t\Software\Zebra Setup Utilities\...

6. Run the setup application Setup.exe and follow the installation instructions.

7. Power the printer on when prompted. The driver will automatically install.

NOTE: The user may click Manual Install if the printer is not installed successfully.

16.4.3 Configuring the Printer Settings

MD-Stainer Service Manual V1._EN 138/173

 1. Open C:/Program Files (x86)/Zebra Technologies/Zebra Setup Utilities/App

a. Run PrnUtils.exe to launch the Zebra Setup Utilities application

2. Click Configure Printer Settings to launch the Printer Settings wizard.

a. Label Parameters 1.00 inch Width x 0.75 inch Height, Normal Orientation

b. Speed and Darkness 2.0 inch/s, 15

c. Media Tear Off, Feed to Next Label, Default settings

d. Advanced settings Transfer, Web Sensing, 0.00 inch Tear off adjust, 0.00 inch

16.4.4 Calibrating the Media

1. Click Open Printer Tools and click Calibrate Media to perform automatic calibration.

a. The printer’s built-in sensor will feed several labels, and adjust settings to account for
label size, type and gap.

16.4.5 Printing a Test Label

1. Launch the PCStainer UI and login as “Distributor”

2. Go to System Utilities > Settings > 2D Barcode Format

3. Select the printer from the dropdown list under Printer:

4. Adjust the Margins and Darkness if necessary.

MD-Stainer Service Manual V1._EN 139/173

 a. Top Margin: 45

b. Width (dots): 252

c. Left Margin: 12

d. Dark Level: 15

5. Go to Prepare Labels and print a test label.

16.5 Maintenance: Computer

16.5.1 Clean-up Log Files

Overtime, the software may start to run more slowly due to accumulation of log files. It is advised to
delete log files periodically. The user may backup the old log files in a separate folder if desired.

1. Open C:/PathCom/PathComAutostainer/Logs

a. Select all files in the folder and delete.

2. Open C:/PathCom/PathComASGui/Logs

a. Select all files in the ReagentTagData folder and delete.

b. Select all files in the RunSet folder and delete.

c. Select all files in the Scanned Slides folder and delete.

16.5.2 Backup Report Data

1. From the Main screen, click “System Utilities” and open the Tools tab to access the utility.

2. Click “Backup Report Data” to access the backup feature.

3. Select/Enter a date to Backup Report Data Before and click “Backup”.

MD-Stainer Service Manual V1._EN 140/173

 a. To retain the selected data after the backup, select the option: “Keep selected files…”

b. To remove the selected data after the backup, select the option: “Remove selected
files…”

4. Select a folder location where the backup will be saved i.e.: local disk or external flash drive.
Alternatively, the user may create a new folder location by clicking “Make New Folder”. Click
“OK” to proceed.

5. All report data files created before the selected date will be copied to a new folder named
“ReportDataBackup” and the current date.

16.5.3 Backup System Files

To prevent accidental loss of key system files, it is advised to perform routine backup of the PathCom
folder AND before and after protocol/reagent upgrades, software upgrades, scheduled instrument
maintenance service etc.

1. Open the C:/ Drive and copy the entire PathCom folder.

2. Rename the copy. Store the copy to an external flash drive or other external source.

16.5.4 Perform General Computer Maintenance

Many of the computer’s automatic maintenance features are disabled to allow the PCStainer SW to
run without interruption. It is advised to manually perform computer maintenance periodically.

1. Windows Update

2. Antivirus Scan

3. Disk Defragmenter

MD-Stainer Service Manual V1._EN 141/173

MD-Stainer Service Manual V1._EN 142/173
 17 Software
17.1 Software and Protocol Version
Before install the software you must download the last release software and protocols version.

You can download it from the Vitro SharePoint site.

17.2 Software Installation Instruction

1. Before installation, please make a backup of the PathCom folder.

a. Exit all MD-Stainer applications.

b. Copy the Installer Package to the computer.
c. Copy and paste the C:\PathCom folder into Local Disk C:/ for easy recovery if problems are
encountered during the installation process.
We suggest for you to use PathCom-serial number-yyyy-mm-dd as a backup folder name,
where yyyy-mm-dd is the year, month and day, i.e. PathCom-pc12018-2015-0126.

NOTE: You must not remove the C:\PathCom folder. This folder is used during the
installation of MD-Stainer system software and it must be present for the installer to be
able to restore all current configurations of the system.

2. Uninstall existing software.

Open the Installer Package and double click UninstallPathCorn.vbs

i. Make sure to only click once. It may take a few minutes to start up and complete
configuration.
ii. Never click "Cancel" during the uninstall process. Doing so will result in data loss.
b. Make sure to click "Yes". Allow Changes, when prompted by the Windows User Account
Control. c. Click "OK" on the popup "PathCom SlideStainer Uninstalled" to complete the
uninstall process

3. Install new software.

a. Open the Installer Package and double click Instal[PathCom.vbs

i. Follow the instructions provided by the software setup wizard.
b. Make sure to click "Yes", Allow Changes, when prompted by the Windows User Account
Control.
c. Click "OK" on the popup "PathCom SlideStainer Installation Finished" to complete the
installation process.

MD-Stainer Service Manual V1._EN 143/173

 4. Post installation configuration.
a. Open the installer Package. If you see an AdditionalFiles folder in the installer, go through
the following steps of Post installation configuration, otherwise, skip the Post installation
configuration.
b. Please copy each file in the AdditionalFiles folder into the corresponding folder in
C:/PathCom. If the files exist on the system already, overwrite the existing files.
i. Copy <insert file name> into C:/PathCom/PathComASGui/Data ii.
Copy<insert file name>into C:/PathCom/PathComAutoStainer/Data
. etc
c. Log on to the new software and refresh all the protocols.

5. Install and Update protocols

The protocols are released separately with the system software. To make sure you are using
current version of protocols, check the protocol version on your system. If your system is running
older version of protocols, please use the PRManager to update your protocols to the current
version.
For update the protocols go to C/PathCom/PathcomASGUI/Data and replacement.

17.3 Troubleshooting: Software

17.3.1 Symptom: Computer lost all calibration data and system settings.
a. Cause: An essential system file was accidentally deleted or corrupted. Windows performed an
automatic repair with default installer files, overwriting all current system files.

Solution:

b. Cause: Installation failed and Windows attempted an automatic repair. System files were
replaced with default installer files.

Solution: Retry installation.

c. Cause: Out-dated desktop shortcut for PCStainer SW was not deleted. Windows performed
an automatic repair with default installer files.

Solution: Remove all old desktop shortcuts. Restore backup directory and reinstall the current
version of software.

17.3.2 Symptom: System aborted or froze during the run.

a. Cause: Cause may vary. Software bug, intermittent error or user error.

Solution: Do not immediately close the application if possible. Collect some key information
about the error to aid in troubleshooting:

i. Take a screen capture of the Gantt chart. Click Print Screen on the keyboard
and open MS Paint. Paste the screen capture and save the file.

MD-Stainer Service Manual V1._EN 144/173

 ii. Log file. Open C:/PathCom/PathComAutostainer/Logs and copy the most
recent run log file.

iii. RunSet file. Open C:/PathCom/PathComASGui/Logs/RunSet and copy the

most recent Runset file.

Contact and send to MD-Stainer Technical Support for assistance/error diagnosis.

Power on/off the system and reboot the computer.

17.3.3 Symptom: System repeatedly aborts or freezes over several runs.

a. Cause: User error.

Solution: Verify the protocols. All protocols must be individually saved in the PCASGui Protocol
Editor or saved in the PCStainer Protocol Editor.

Send protocols to MD-Stainer Technical Support for verification.

b. Cause: Hardware failure.

Solution: Verify the electrical boards and wires. Check for leaking on the module PCB boards
and the connectors on the backplane PCB board. Check for loose cable connections on the
robot, pumps, communications board etc. Contact MD-Stainer Technical Support for
assistance/error diagnosis.

17.3.4 Symptom: Yellow warning message displays on the slide map during the run.
a. Cause: Low or High Temperature warning. Heater may have failed.

Solution: Perform a heater check and/or verify the actual temperature of the module with an
IR probe.

b. Cause: An error occurred during the run that may affect the staining results.

Solution: Record the error and send the log file to MD-Stainer Technical Support for
assistance/error diagnosis.

17.3.5 Symptom: Software displayed unhandled exception message or another Windows

error.
a. Cause: Cause may vary. Software bug, intermittent error or user error.

b. Solution: Do not immediately close the application if possible. Collect some key information
about the error to aid in troubleshooting:

i. Take a screen capture of the error. Click Print Screen on the keyboard and
open MS Paint. Paste the screen capture and save the file.

MD-Stainer Service Manual V1._EN 145/173

 ii. Log file. Open C:/PathCom/PathComAutostainer/Logs and copy the most
recent run log file.

iii. RunSet file. Open C:/PathCom/PathComASGui/Logs/RunSet and copy the

most recent Runset file.

Contact and send to MD-Stainer Technical Support for assistance/error diagnosis.

Power on/off the system and reboot the computer.

17.3.6 Symptom: Autostainer server stopped working, not responsive, closed or frozen.
a. Cause: File folder options were changed or user performed software installation while the
server was running.

Solution: Restart the server.

b. Cause: Intermittent error, software failure or sudden power off.

Solution: Restart the server.

c. Cause: Server was improperly closed and became corrupted.

Solution: Recover settings using a backup. Go to C:\Users\PathCom\AppData\Local\PathCom

and delete the current working copy of the server i.e.:

PathComAutostainer.exe_Url_efx1l0mial30flbawmodjp5soyfpz1m5

17.3.7 Symptom: Software is not responsive.

a. Cause: Instrument lost communications or home position(s).

Solution: Go to System Utilities > Tools and click “Initialize System”.

b. Cause: Server error, lost connection, did not open properly or stopped working.

Solution: Go to Scan Reagents and click “Cancel” to restart the server.

c. Cause: Software crash. Overload memory/CPU.

Solution: Close the main user interface and login again.

d. Cause: Computer crash. Overload memory/CPU.

Solution: Reboot the computer and login again.

i. Be sure to wait a few minutes after booting up the computer before logging
into PCStainer software. Some start up programs may interfere with proper
start-up of the software.

MD-Stainer Service Manual V1._EN 146/173

 e. Cause: Computer lost all calibration data and system settings.

Solution: Refer to 17.3.1 Symptom: Computer lost all calibration data and system settings.
Troubleshooting Overview

17.4 Staining Troubleshooting

The following trouble shooting guide has the assumption that all reagents are provided by
Manufacturer, and that the user is running the standard IHC protocol or manufacturer recommended
protocols.

17.4.1 Weak Staining

1. Weak staining across all slides:

a. Verify Probe Z1 and Probe Z2 positions (SP1-Z1 Calibration and SP1-Z2 Calibration
feature at System Utilities)

i. Bended Z2 probe may cause extracting not clean, which will lead weak
staining and/or high background also

ii. Z1 incorrect position may cause the reagent overflow, which mean less
reagent volume is in the chamber

b. Verify the detection reagents (DAB and/or Polymer etc.)

i. Different detection lots?

ii. Change detection supplier?

iii. Detection solutions lose activity?

c. Verify the tubing cleanliness

i. Dirty tubing will impact the reagent/buffer flow (run Tubing Cleaning kit)

d. Verify the chamber cleanness

i. Dirty chambers will cause weak and uneven staining (clean chamber)

e. Verify IHC default protocol or protocols (key steps)

i. TR temperature and incubation time

ii. Ab incubation temperature and time

f. Change of paraffin vendor change or tissue fixation

i. May need modify the dewaxing protocol (temperature and time)

2. Weak staining with one or a few random slides:

MD-Stainer Service Manual V1._EN 147/173

 a. Verify if the chambers are cracked

b. Verify if the chambers are clean

c. Verify extraction with the Extracting Test

i. Partial extraction or intermittent bad extraction?

3. Weak staining with a specific antibody:

a. Verify the protocol

i. Some Abs may require protocol modifications and/or a special protocol (i.e.
increase TR temperature to 103c)

ii. Refer to the qualified Abs list for more information.

b. Verify the reagent volume

c. Verify the Abs

i. Ab lost activity?

d. Change Ab vendor or Ab clone-related?

4. Weak staining with one type of tissue:

a. Modify the protocol and/or create a special protocol for this tissue

5. Weak staining with a specific module:

a. Perform extracting test, recalibrate as needed

i. Verify Extract (Height) position

ii. Run Extracting test protocol

b. Compare heating temperature and the heater surface temperature

i. At 100c, the variation shall be within 3 degrees

c. Heater surface cleanliness

i. Residue and salt may cause lower temperature and uneven heating

17.4.2 Uneven Staining

1. Partial staining: the higher part of the slide (towards the label area)/big tissue is not stained

a. Check the tissue location to verify if the tissue is placed outside of the staining area

MD-Stainer Service Manual V1._EN 148/173

 i. Refer to 11.2. Recommended Staining Area

b. Verify the reagent bottle and leftover reagent volume

i. Insufficient reagent in the chamber will make the staining area smaller, and
may also cause weak staining

c. Check for cracks on the chamber

i. A cracked chamber will usually make the staining area smaller, but may also
cause high staining background

d. Verify the agitation heights for A2/A5 and A6/A7

i. Refer to 11.3. Calibration: Module Agitation Heights

ii. A2/A5 and A6/A7 too high will make the staining area smaller

iii. A2/A5 are usually the key heights for determining the staining area

2. Patching: some areas within the same tissue have noticeably weaker staining

a. Chamber surface cleanness

i. Refer to 11.5.1. Chamber Cleaning and Replacement

b. Chamber cracked?

c. Verify the key steps of the protocol

i. Retrieval solution temperature and time (too high or too long)

ii. Agitation frequency is too slow may cause uneven reagent sit on the tissue
surface too long

d. Other

i. A6/A7 too low may cause the reagent uneven spreads on tissue

ii. Variation of the tissue fixation

iii. Thickness variation of tissues

17.4.3 Staining Background

1. Chamber marks: tissue slides with a complete and/or partial chamber pressing mark

a. Clean chamber, especially the gasket around the chamber surface

MD-Stainer Service Manual V1._EN 149/173

 2. Tissue slide has a light hue (sometimes uneven):

a. Reagent stays in a chamber too long after DAB

i. Use the “delay start” function

b. Retrieval temperature too high and/or TR time too long

3. High Background across all slides within a run:

a. DAB reagent expired with precipitates

b. Waste extraction is not clean

i. Verify Z1/Z2 probe positions

c. Insufficient buffer

d. Tubing dirty (residues and/or wax in the tubing)

4. High Background for an individual slide:

a. Chamber cracked or not?

b. Chamber cleanliness

c. Waste extraction is not clean

i. Verify the Extraction position

17.4.4 No Staining
1. All slides are having no staining:

a. Verify all common reagent bottles and volumes

i. Load the Slide Map file in System Utilities

ii. Load the Reagent Map file in the Reagent Check screen.

b. Verify all the common reagent labels and scanned reagent names to see if there is
anything mismatched

i. Detections: HRP, DAB etc.

ii. DS and TR solutions

c. Verify that all the common reagents are at the correct positions on the Reagent Map
for any manually assigned reagents

d. Initialize the system to observe the Pump1 and Pump2 buffer flow

MD-Stainer Service Manual V1._EN 150/173

 i. Verify if the tubing is not blocked or two pumps are functional

2. One or several slides have no staining while the others have stained well:

a. Verify the reagent bottles and volumes

i. Insufficient reagent will cause the first few slides of a group to be unstained
(depending on how much reagent is missing) or cause weak staining or
smaller staining area

b. Check the chamber for cracks

i. A small crack may cause weak staining, less staining area, or staining
background high

c. Verify LLS (liquid level sensor) function

i. The smaller volume of Ab left in the bottle, the higher chance there is of a
“no staining” problem

3. One specific Ab with negative staining on the positive control tissues:

a. Check the qualified ab list to verify

i. If this Ab is on the qualified list

ii. If there is specific protocol requirement for this Ab

b. Work with the instrument and Ab manufacturers to modify the protocols or make a
special protocol for this Ab

17.4.5 Other Issues

1. Paraffin residue remains on the tissue:

a. Heater Check

i. If the heating function has failed, wax will not be removed cleanly

b. Modify the dewaxing protocol

i. Increase the dewaxing temperature and volume

2. The staining is too strong for some Abs:

a. Lower TR temperature

b. May use low-pH TR solution

MD-Stainer Service Manual V1._EN 151/173

 c. Use DW buffer instead of DS2

3. The tissue morphology for some tissues is not optimal:

a. May use low-pH TR solution

b. Lower TR temperature

4. Some tissue has endogenous peroxides with low-pH TR solution:

a. Use H2O2 block to replace DS2

5. Some Abs require enzyme pre-treatment:

a. Use enzyme to replace TR solution, lower the incubation temperature to 37c or

optimal temperature for this Ab/enzyme

b. Use enzyme to replace DS2 (plus temperature retrieval)

17.5 Instrument Troubleshooting

17.5.1 General Troubleshooting

Tip: To recover from an error/problem, first try

1) restarting the server

2) restarting the PCStainer SW

3) restarting the computer

4) powering cycling the instrument.

17.5.2 Symptom: Instrument does not power on.

a. Cause: A cable is disconnected or loosened. No LED lights on electronic boards are on.

Solution: Reconnect the cable 1) power cord, 2) UPS power cord, 3) main power supply cable
on communications board.

b. Cause: Power supply failure. No LED lights on electronic boards are on. Power supply fan is
off.

Solution: Replace the power supply.

c. Cause: Power switch malfunction. LED light on communications board is on.

Solution: Replace the power switch.

MD-Stainer Service Manual V1._EN 152/173

 17.5.3 Symptom: Cannot connect to the instrument.
a. Cause: Server lost connection or did not start up correctly.

Solution: Close and reopen the server by click “Scan Reagents” on the main interface.

b. Cause: USB lost connection or did not make a proper connection.

Solution: Reset USB connection by unplugging and plugging in the cable.

c. Cause: Computer went into sleep or hibernation mode.

Solution: Adjust power settings to never go into sleep or hibernation mode. Restart the
computer.

d. Cause: Computer lost all calibration data and system settings.

Solution: Refer to 17.3.1. Symptom: Computer lost all calibration data and system settings.

17.5.4 Symptom: Cannot connect to one or more devices.

a. Cause: COM Port number changed.

Solution: Restart the computer.

b. Cause: Device failure.

Solution: Refer to Troubleshooting for 1) Module, 2) Robot, 3) RFID Reader, or 4) Barcode

Reader.

c. Cause: Loose cable connection.

Solution: Verify Internet cable for Slides. Verify Robot comm. cable for Robot. Verify RFID
comm. cable for RFID Reader. Verify USB Serial converter cable for Barcode Reader.

d. Cause: Communications Board failure.

Solution: Replace the Communications Board.

e. Cause: USB Cable malfunctions.

Solution: Plug and unplug the USB cable. Restart the computer. Replace the USB cable.

f. Cause: Computer USB Port malfunctions.

Solution: Restart the computer. Try using a different USB Port or a different computer.

g. Cause: Computer lost all calibration data and system settings.

Solution: Refer to 17.3.1. Symptom: Computer lost all calibration data and system settings.

MD-Stainer Service Manual V1._EN 153/173

 17.5.5 Symptom: Instrument running very slow or appears “frozen”.
a. Cause: A background program is interfering with the PCStainer SW.

Solution: Disable all background programs i.e.: Windows Update, Antivirus, Disk
Defragmenter.

b. Cause: Broken Network connection to server causes delays.

Solution: Disable network connection or reconnect to the network.

c. Cause: Broken communications to a module. Causes Slide terminal to reset repeatedly.

Solution: Replace or omit the problem module from the staining run.

d. Cause: Broken communications to the backplane PCB. Causes Slide terminal to reset
repeatedly.

Solution: Omit the problem module position until it can be repaired.

e. Cause: Protocol parameters exceed SW limitations. Causes Slide terminal to reset repeatedly.

Solution: Adjust the protocol to meet the required parameters.

f. Cause: Broken communications to the robot. Causes Robot terminal to reset repeatedly.

Solution: Power cycle the robot to clear the error. Consult Manufacturer for further support
if the problem persists.

Refer to the relevant troubleshooting sections for the Module, Robot, RFID Reader, Barcode Reader,
Tubing, Pumps and Software for further details.

MD-Stainer Service Manual V1._EN 154/173

 18 Miscellaneous
18.1 Outer Housing Disassembly and Assembly
The outer housing may need to be disassembled to perform maintenance/repair services.

1. Disassemble the Outer Housing

a. Power off the instrument and unplug the USB cable and power cord.

b. Remove the Back panel.

c. Remove the entire Top panel with Door attached.

d. Unscrew the Interlock Switch cover from the Left side panel. The Interlock Switch and
are attached.

e. Remove the Left side panel.

f. (If necessary) remove the Right side panel.

g. Disconnect the Power Switch cable from the Communications board.

h. (If necessary) remove the Front panel.

2. Reassemble the Outer Housing

a. Verify all connections and pump/robot/slide/RFID/barcode functions.

b. (If necessary) reinstall the Front panel.

c. (If necessary) reinstall the Right side panel. Be careful not to damage the power switch
cable.

i. Feed the free end of the power switch cable through the rectangular opening
on the Backplane PCB support located towards the back under the base of the
instrument.

MD-Stainer Service Manual V1._EN 155/173

 Power Switch

ii. Reconnect the power switch cable to the Communications board.

d. Power off the instrument and unplug the USB cable and power cord.

e. Reinstall the Left side panel. Be careful not to damage the interlock cable.

i. The Interlock Cable should be positioned in the opening between the deck
plate and the left panel.

f. Reinstall the Interlock Switch cover.

g. Reinstall the Top panel with Door attached.

h. Adjust the alignment of the housing parts before fully tightening the screws.

i. Verify that the door can open/close freely. Adjust the door hinges if necessary.

j. Verify the door lock and interlock function.

k. Verify all connections and pump/robot/slide/RFID/barcode functions.

l. Reinstall the Back panel.

18.2 Power Supply Replacement

The power supply may need to be replaced in the event of a power supply failure in which 1) the
power switch signals an error with a continuously flashing light or 2) the instrument completely fails
to power on.

1. Verify the Power Supply Failure

a. Power off the instrument and power supply.

b. Wait 30 minutes to an hour before attempting to power the instrument back on.
Sometimes the power supply must auto-shutoff and reset after encountering a short,
power surge or sudden interruption of power.

c. Remove the Back panel and verify the connection on all power cables:

MD-Stainer Service Manual V1._EN 156/173

 i. The 24 pin main power supply cable should be fully seated in the connector
on the Communications board.

ii. The 6 pin main power cable (12V IN) should be fully seated in the connector
on the 12-24V Power Converter board (left).

iii. The 2 pin power cable (24V OUT) should be fully seated in the connector on
the 12-24V Power Converter board (right).

iv. The 4 pin main power cable should be fully seated in the connector on the
RFID Adapter B board.

2. Remove the Power Supply

a. Unscrew the 2 screws securing the power supply to the back face of the equipment
pan.

b. Disconnect the main power supply cable from the Communications board.

c. Push back on the power supply and lift it up slightly to pop it out of position.

d. Pull the power supply out through the cut-out on the equipment pan.

e. Detach the 3 cables connected to the Backplane PCB, Communications board and 12-
24V Power Converter.

MD-Stainer Service Manual V1._EN 157/173

 Main power supply cable

3. Replace the Power Supply

a. Attach the 3 cables to the new power supply.

b. Place the new power supply through the cut-out. Make sure the wires are tucked
neatly behind the power supply.

c. Reposition the wires until the power supply sits flat on the equipment pan with no
wires underneath.

d. Connect the 24 pin main power supply cable to the Communications board.

e. Hold the power supply in position with a small screwdriver while retightening the two
screws on the equipment pan.

f. Verify all instrument functions, including the pumps, robot, slide, RFID reader,
barcode reader and fans.

18.3 Communications Board Replacement

The communications board may need to be replaced in the event of a communications board
malfunction in which 1) the ports cannot be detected, 2) there is a loss of power to certain instrument
components or 3) there is a loss of communication to certain instrument components.

1. Remove the Communications Board

a. Power off the instrument and power supply. Unplug the power cord and USB cable.

b. Remove the Back panel.

c. Unscrew the 4 screws securing the 4 corners to the standoffs on the equipment pan.

d. Unplug all cables.

i. Robot Communications cable (RS232)

MD-Stainer Service Manual V1._EN 158/173

 ii. RFID Communications cable (RS232)

iii. Power switch cable

iv. Internet cable (for communications with module backplane)

v. Barcode Reader USB-Serial Converter cable

vi. Interlock cable (4 pin)

vii. 24V power converter cable (2 pin)

viii. Main power supply cable (24 pin)

i. Robot Comm.
viii. Main power ii. RFID Comm.

iii. Power

iv. Internet

v. Barcode

vi. Interlock

vii. 12-24V

2. Install the Communications Board.

a. Plug in all cables in the original configuration.

b. Secure the 4 corners of the board to the standoffs with the 4 screws.

c. Set the new device addresses for the Slides and Robot.

d. Reassign the COM port number (if needed) for the Barcode Reader and RFID Reader.

MD-Stainer Service Manual V1._EN 159/173

 e. Verify instrument function.

18.4 Other Electronic Boards Replacement

Not recommended. Please consult MD-Stainer Technical Support for assistance before proceeding
with repairs.

1. Several key electronic boards are housed beneath the XYZZ system. The air baffle has a cut-
out to allow easy access to the electronic boards. Use a small screwdriver to unscrew the
boards from below the air baffle:

a. 12V-24V Power Converter

b. RFID Adapter B. Located underneath the power converter.

c. Interconnect PCB. Refer to robot manufacturer’s guidelines.

d. CCU for XYZZ. Refer to robot manufacturer’s guidelines.

e. X Controller. Refer to robot manufacturer’s guidelines.

2. The RFID Adaptor A is located on the YZZ assembly on the XYZZ system.

3. The Backplane PCB is located under the deck plate. The process to replace the backplane
board requires removal of all 36 modules/wash stations/deck plate and full instrument
calibration. It is not recommended.

X Flex

MD-Stainer Service Manual V1._EN 160/173

 X Flex X Flex

Cable pump interface

Robot Comm. Cable pump interface

C
12-24V Converter

MD-Stainer Service Manual V1._EN 161/173

 RFID Ribbon
12-24V Converter

Power
supply
Power
supply
RFID Comm.

Fan Fan

MD-Stainer Service Manual V1._EN 162/173

MD-Stainer Service Manual V1._EN 163/173
 19 GENERAL FAQs and How-Tos
19.1 FAQs

19.1.1 Part I: Hardware

Question: Can I restart the PC while the Stainer is running?

Response: No, the run will be interrupted.

Question: Why is it important to check the vials before each run? Shouldn’t the instrument know when the
vials are empty?

Response: Because all the test number information is recorded on RFID tags as the liquid level sensor can only
detect the level but not the amount of reagent.

Question: Can I leave the caps on if I simply want to scan the reagents?

Response: No, the caps must be removed before scanning to prevent bending the Z1/Z2 probes. The
instrument does not detect if the caps have been removed from the vials.

Question: What happens if there is a power outage or power surge? Will the Stainer remember where it was
in a staining run?

Response: No, it will not. We recommend the use of filtering UPSs.

Question: How often should I restart my instrument? Or turn it off?

Response: Weekends or any other extended period of inactivity.

Also, restart the instrument and computer if the system cannot recover from an error.

Question: What is the proper procedure to power off the instrument?

Response: Click Exit to exit the main interface. After exiting, press and hold the power button on the side of
the instrument. Finally, flip the switch to the power supply on the back of the instrument to completely power
off the instrument. Shut down the computer. The computer must be restarted every time the instrument is
fully powered off.

Question: Can I run other programs while the instrument is running?

Response: No, do not multitask i.e.: run background programs, perform SW updates, run Antivirus SW or
connect to the Internet while the instrument is in operation. Doing so may cause unexpected crashes of the
SW.

Question: Can I use a screen saver or modify any other computer settings?

Response: No, never turn off the display or put the computer in sleep or hibernation mode while the
instrument is in operation. Doing so may cause unexpected crashes of the SW.

MD-Stainer Service Manual V1._EN 164/173

Question: What happens if I accidentally disconnect the USB from the computer to the instrument while it is
running?

Response: The computer must be connected to the instrument at all times in order for it to run. Reconnect
the USB and click Exit to stop the run. The computer must be restarted to refresh the ports. Always restart the
computer when the USB is disconnected.

Question: How often should you calibrate the Stainer?

Response: Recalibrate the robot after changing the tubing or after observing poor extraction/misalignment
with the chimney, if the probes become misaligned to the chamber chimneys, if staining gradients appear, or
if any physical trauma happens to the robot.

Verify and recalibrate the modules after changing a heater or every six months, as needed.

Question: Can a PC run more than one Stainer together?

Response: No.

Question: What size slides can be used on Stainer?

Response: Material Glass, ISO 8037/1

Dimensions (mm)

Width 25–26.0 mm

Length 74.75–75.5 mm

Thickness 0.95–1.1 mm

How much fluid do the Stainer containers hold?

Response:

Container Stainer (Capacity)

Buffer Bottle 2 Litres

Standard waste Customer choice

Hazardous waste Customer choice

15ml Vial 16.5ml

Question: Can the Stainer detect liquid levels in bulk containers?

Response: No.

MD-Stainer Service Manual V1._EN 165/173

Question: Can the lid be open while the Stainer is running?

Response: The lid will automatically close and lock during a run for safety reasons.

Question: Can I use less than 150ul dispense volume on Stainer?

Response: Yes, the system works from 95ul up to 130ul.

19.1.2 Software
Question: A barcode does not scan. How do I enter it as a protocol?

Response: You can manually select the slide and then assign the protocols from the main screen.

To avoid scanning errors, try closing the door and making sure the barcode label is not wrinkled when applied
to the slide.

Question: An RFID does not scan. How do I enter it as a reagent?

Response: You can manually assign the reagent (for a limited number of tests).

Question: How often should I backup the database?

Response: User’s decision. It is also advised to back up whenever a significant change is made to the protocols
and after any software upgrade.

Question: Can Stainer run IHC and ISH at the same time?

Response: Yes.

Question: Is there a report that gives a customer the number of tests used for a particular detection system
(like Reagent Usage report that only gives antibodies, probe and ancillary information)?

Response: No.

Question: How can I tell what step my instrument is running and how much time remains to finish the run?

Response: View the slide map on the main user interface, each slide is marked with the current step.

Check the countdown clock at the top of the screen to view the remaining time.

Question: I saw a yellow error message displayed on the slide map during the run. What does it mean?

Response: The system encountered an error while processing that slide. The staining results may be impacted.

Question: My run did not finish successfully and the tissue didn’t stain. Can I re-run the same slide?

Response: Yes, but you have to evaluate the condition of the slide and possibly the step that stopped the
session.

Question: Can I select the starting time for my run? How?

MD-Stainer Service Manual V1._EN 166/173

Response: Yes, click on the delay start button and enter the ending time.

NOTE: It is not recommended to use delayed start with fresh tissue slides that must stay wet or
require or slides that do not require dewaxing.

Question: Can I abort the staining run? How?

Response: Yes. Click “Exit” on the main user interface. In case of an emergency, power off the instrument or
disconnect the power. If you stop a run, you will need to re-start the session again.

19.1.3 Protocols
Question: Can I modify a protocol after the run has begun?

Response: No.

Question: What parameters can I adjust for an individual protocol?

Response: The user may adjust the DS2 option, TR option, TR temperature, Ab incubation temperature and
time.

Question: How do I revert to the manufacturer’s original settings?

Response: Select the protocol and click “Go Back to Manufacturer Default”.

Question: How do I add a new IHC Abs protocol to the system?

Response: Add the new Ab as a new reagent in the Reagent Editor.

The protocol will be automatically generated and can be modified in the Protocol Editor.

19.1.4 Chambers Technology

Question: How do the chambers work?

Response: They exploit the repeated spreading of the reagents onto the slides, thereby increasing the binding
of the reagents.

19.1.5 Reagents and Waste

Question: Can I change or fill buffer after the run has begun?

Response: Yes, but only when the system isn’t dispensing wash buffer. It is not recommended, as this may
cause bubbles to form in the line. This can be avoided by checking the container before the start of every run
or at least once daily.

Question: Can I remove the primary antibodies before the run has completed?

Response: No, the door will be locked.

MD-Stainer Service Manual V1._EN 167/173

Question: What happens if there are not enough reagents in the detection kit?

Response: During the reagents check the SW will inform the user that there is an insufficient amount of
reagent. The user can add an extra vial and rescan.

Question: Does the software allow the user to start one reagent and finish it off completely before using a
second one?

Response: Yes. Load two reagent vials, one partially full and the other full. The Stainer will automatically draw
the reagent from the partial vial first.

Question: Can I manually combine the residual reagent from several RTU containers and use it up?

Response: Yes, but do so at the user’s risk. There will be no traceability through the RFID tags/system tracking
when using manual assignment. This feature may be restricted by certain distributors.

Question: Can I use another ‘dewax’ reagent other than the one specified?

Response: No.

Question: Can I change the retrieval temperature?

Response: Yes. Generally, 103C is the highest retrieval temperature used to get good staining results.

Question: Can I use a different retrieval solution?

Response: No.

Question: Can you change the assigned expiration date for an antibody?

Response: Not for antibodies provided by the distributor.

Users can reprogram their own antibody vials using the RFID Editor.

Question: How can I check that there are a sufficient number of tests for all my slides?

Response: The user can read the number of tests remaining from the RFID tag. After the reagent check, the
insufficient reagents are identified by colour code. It is always a good idea to visually check the level of the
reagents in case there is a leakage/spill or insufficient volume.

Question: Does Stainer know if you spill a reagent?

Response: No.

Question: Does Stainer know if you spill a bulk reagent?

Response: No.

Question: How many different kits/protocols/retrievals/antibodies can I run together?

Response: The limit factor is the number of the positions available in the reagent rack. The maximum number
of protocols that can be run at one time is 36(one protocol per module).

MD-Stainer Service Manual V1._EN 168/173

Question: Can I assign a reagent manually?

Response: Yes. This feature may be restricted by certain distributors.

Question: Can I run two different detection systems?

Response: Yes.

Question: What is the dead volume?

Response: The dead volume is a small amount of reagent left in the container. It ensures that Stainer can
aspirate enough reagents to dispense onto the slides.

Question: How does the SW calculate the Ab volume needed?

Response: For 15ml vial, required volume=No. of tests x 130ul x 1.08 + 1ml dead volume

Question: Can I reuse the vials?

Response: Yes. The RFID tag may need to be reprogrammed or replaced.

Question: What happens if the detection system or antibody runs out mid run?

Response: There may be an impact on staining results. The first one or few slides of the group may be
negative/partial/weakly stained.

Question: What happens if I forget to empty the waste containers before I start my run?

Response: The waste liquid will overflow, but the system will continue to run.

Question: Can the non-Hazardous waste go down the sink?

Response: Check with your local authority on the disposal of the non-hazardous waste. Different regions have
different regulations.

Question: Can I remove a waste container while the Stainer is running?

Response: Yes (if necessary), it is best to wait until the Stainer is incubating and not dispensing any reagent.

19.1.6 Cleaning and Maintenance

Question: What if I accidentally bend a probe?

Response: Go to System Utilities in the main user interface and click SP1-Z1 Calibration or SP1-Z2 Calibration.

The robot will move the selected probe to the first module. Gently bend the probe back to the proper position.

Question: How often should I clean the chambers?

Response: Refer to ¡Error! No se encuentra el origen de la referencia.. ¡Error! No se encuentra el origen de

la referencia..

MD-Stainer Service Manual V1._EN 169/173

Wipe the chambers with an alcohol pad after each run.

Run the “Clean Chamber” protocol and deep clean with Bleach every 3-5 runs.

Deep clean with Bleach can be performed 10-15 runs (if running Clean Chamber regularly).

Question: How do I clean the aspirating probe?

For the outside of the probe, wipe away any salt/build-up with an alcohol pad.

For the inside of the probe, follow tubing cleaning procedure.

Question: How often should I clean the tubing?

Response: Refer to ¡Error! No se encuentra el origen de la referencia.. ¡Error! No se encuentra el origen de

la referencia..

Perform as needed or at least every 6 months/150 cycles of staining.

Use the Tubing Clean feature. Use bleach to remove DAB precipitate and SlideBrite to remove wax build-up.

Question: How often do I have to change the aspirating Probe?

Response: It should last for several years.

Question: How often do I have to change the chambers?

Response: Cracked chambers must be replaced immediately. The chambers should last 50+ runs on average.
The chamber may become damaged prematurely if the proper handling/cleaning procedures are not followed.

Question: How often should I change the tubing?

Response: During the scheduled technical support maintenance every 6-12 months, or every 150-300 cycles
of staining.

19.2 HOW-TOs

19.2.1 How to update the Reagents and Protocols in MD Stainer Software

Before to the updating process make a backup of the MD Stainer Software folder.

Once updating these files, the MD Stainer Software can use any existing protocol.

Any error or missing step in this protocol could cause malfunction on the Stainer process and software.

• Copy the files with the last version of the Protocols and Reagents from the SharePoint site:

o Protocols.xml

o Reagents.xml

MD-Stainer Service Manual V1._EN 170/173

 o ReagentDispenseFactors.xml

o ReagentDrawFactors.xml

And replace them to the folder C:\Pathcom\PathcomASGui\Data

• Open the MD Stainer Software

• Go to the System Utilities > Settings and click on Save All Customizations button.

• Go to System Utilities > Editors and click on Protocol Editor

MD-Stainer Service Manual V1._EN 171/173

 • Click on HRP Super and elect all the records clicking on the top left corner.

• Click on Refresh Protocols with Customizations Button

MD-Stainer Service Manual V1._EN 172/173

 • Click on Return Button and close the System Utilities

MD-Stainer Service Manual V1._EN 173/173