@Heartyhar the colouration that you see when not using the OpenFlexure software is because of the built in hardware design and software corrections to give an image with good colour reproduction when using the intended lens in its intended use as a camera with a built in IR filter. The No-IR camera I think does give the pink cast that you see when used as a camera. Using the camera sensor as a microscope changes the colour casts. The calibration function in the OpenFlexure software measures the colour and shading on an empty image and then corrects for it, as in the images in OpenFlexure Microscope Stack and Scan Video - General - OpenFlexure Forum
@dgrosen if you are on the latest software 2.10.0 or 2.10.1 then the colouration is surprising and we need to work out why it is happening. There were inconsistencies in calibration in version 2.9, which should all be fixed in 2.10.
Note, the pre-built SD card images are still dated 2021-06-17, which is before the v2.10 release. You will need to upgrade once you have built a new microscope.
sudo ofm update
sudo ofm upgrade
(see Software release v2.10.0 - Announcements - OpenFlexure Forum)
[edit: I missed your previous post @dgrosen. The upgrade from v2.9.3 to v2.10.1 should make it all work.]