Usually the “Unable to detect a soma there” message there (when your eye can clearly see one) refers to the sensitivity slider being too low/too far to the left. Assuming you’ve already tried moving it to the right, there are a couple other things to check:
- Hold the control key and use the scroll wheel on your mouse to make the target slightly larger than your cell (this shouldn’t directly impact whether a soma is detected or not, but it’ll help make sure the actual soma that gets dected is the right size).
- Try using the image adjustment window’s histrogram to change the white point or the gamma of the channel you’re looking at. Sliding the white point slider to the left should decrease the total dynamic range of the image and make anything faint a lot brighter.
- Double check that the scaling of your image is correct - in the 2D window, use Trace>Measure Line, measure a soma and make sure it’s 20 microns or so.
If it’s still not working, open a support case here: https://www.mbfbioscience.com/open-support-case