I inherited the UK Virtual Microscope project pre-covid with only user-level expertise and (very) limited funds. After replacing a dead iMac with an equally aged one hooked up to a Leica DMRP 'scope and DFC490 camera, the software works as expected but the images are very poor (see screenshot). Same degradation regardless of objective used. This is probably a very simple and obvious problem, but is it the camera, the 'scope itself, or maybe the firewire connector? The asymmetry makes me think it is some misalignment of optical components, rather than a software issue (Leica Firecam 3.4).
Apologies for this basic newbie post - any pointers would be welcome!
Cheers, Tom
Hello @tomargles and welcome to the forum,
You say the degradation (I assume we are talking about the uneven shading across the field) is the same for any objective. This suggests that it is an issue with camera background flat field correction.
I am not familiar with that specific microscope system but, in general, you need to make dark field and flat field images and have these applied to your camera feed to correct for such things. I can’t tell you the specifics of how to do it with your system but perhaps you can explore the topics of dark field image and flat field image (and ‘correction’ for the same) in your user manuals or the software help files.
If you want some general background knowledge on these topics you can see my video on YouTube here:
I hope this points you in the right direction.
PJT
Hi PJT,
Thank you, I should have thought of that - we routinely run a ‘Set shading’ correction for each scan on our other scope, which acquires stitched mosaics of entire thin sections, to eliminate banding effects. It wasn’t in the workflow for this rig, maybe because we only snap single images. There may have been a default correction applied in the settings somewhere which was erased when the software was re-installed. I’ll have a dig around; that correction wasn’t obvious in the camera settings but it must be there somewhere!
Cheers,
Tom
I tried adjusting the white balance (which is not well named, it is actually a shading correction) but further investigation of optical components uncovered a polarising filter on a sliding bar assembly that was slipping slightly, resulting in dark vignetting on the left side of the image.
But, after correcting that and re-adjusting the white balance several times, I could not eliminate the banding. Not too noticeable under plane polarised light (brighter images) but very noticeable on dark areas- - see below. Persisted when I unmounted the camera and imaged my phone torch instead, so it does seem to be related to the software, sensor or cable… Colour banding is always vertical but bands change (thickness, spacing, number), though always on left side of image. Most obvious in image below down left third of image, but fainter bands visible in the black area just left of centre.
