Webb's instruments are contained within the Integrated Science Instrument Module (ISIM) which is one of three major elements that comprise the James Webb Space Telescope Observatory flight system. The others are the Optical Telescope Element (OTE) and the Spacecraft Element (Spacecraft Bus and Sunshield).

Integrating four major instruments and numerous subsystems into one payload, the ISIM, was a daunting endeavor. To simplify integration, engineers divided the ISIM into three regions.

The "region 1" component is the cryogenic instrument module. This chills the detectors down to 39 K, a necessary first-stage cooling effort so that the spacecraft's own heat doesn't interfere with the infrared light (a form of heat) detected from distant cosmic sources. The ISIM/OTE Thermal Management Subsystem provides passive cooling. Other devices get the detectors even colder.

The "region 2" component is the ISIM Electronics Compartment, which provides the mounting surfaces and ambient thermally controlled environment for the instrument control electronics.

The "region 3" component, located within the Spacecraft Bus, is the ISIM Command and Data Handling subsystem, with integral ISIM flight Software, and the MIRI cryocooler compressor and control electronics.

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