The coordinates of JWST data are transformed from the raw coordinate system to the science coordinate system.
DMS produces data that has been rotated from the raw (“native” readout coordinate frame) orientations to the science orientations, putting all the detectors in the same orientation with respect to the V2, V3 axes in the focal plane. This requires flipping and rotating the reference pixels and science coordinates for NIRSpec, NIRCam, NIRISS, and FGS. MIRI by design has the same detector and science (X, Y) coordinates so no transformations are needed. The figure below shows with the red box the origin of the raw coordinates of the detector. The green box shows the origin of the science orientation, with the X and Y axis indicated with the black arrows. The lines across the the NIR detectors indicate the regions for each of the four output sublocks (512 × 2048) pixels in size, with the slow scan direction going opposite to the red box parallel to the black lines. The default fast scan directions are indicated with the arrows at the bottom of the NIRISS detector.
The orientation between the spacecraft V2/V3 coordinate system and the FITS science image x/y coordinate system is shown below. The telescope V1/V2/V3 coordinate system is right-handed with +V1 pointing toward the sky and out the page.
JWST technical documents