Hello everyone,
I’m working with diatoms and was looking into possible solutions for improving the standard methodolgy via virtual slides. Commercial slide scanners are very expensive and I’ve discovered this project which seems like a good starting point. Before making an OFM, I have a few questions and I apologize in advance if these have been repeated:
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My main use for it would be to try to scan prepared diatom slides. Diatom slides we use have coverslips that are 20x20mm and I see that the stage travel on the V7 is less than that. Is there a solution to mitigate that, like manually placing the slide a certain way, scanning half, then moving it a bit to scan the other (might be a great misunderstanding on how this works)? Or is changing the size of the components the way to go? Some papers suggest making a scan of the coverslip with an 40x objective and after scan only parts that are abundant with an 100x objective and then stitch those, so I might not need the whole thing but just checking what the limits are.
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I was thinking that the Delta Stage might be more stable for the use case but when looking at the documentation, the BOM and certain parts of the documentation seem to be behind the V7 and being worked on. Should I go with the V7 instead? The reason this is an issue is because sourcing parts is a bit of a challenge where I live, so I’m curious which aspects should be adjusted for the new Sangaboard and the like.
I think that’s it for now, I hope I’ve articulated this well enough. Thanks in advance for the help!
As you suggest, the most straight forward way to scan a larger area is to scan then move the slide and scan a new area. If the 20x20mm coverslip is in the centre of the slide, then you should be able to move the slide enough without it falling off. You might want to have a jig so that you are able to make the areas reliably cover the slide.
Making the physical range of motion with the stage larger is not so simple.
I would suggest that you do use the OpenFlexure Microscope v7 (currently v7.0.0-beta5). As you say the Delta Stage is less advanced in the build instructions etc, and does not include some of the latest electronics.
Two more practical issues: At 100x the field of view is rather small. There will very, very many individual images to cover 20x20mm, which will take a long time. Also you imply that your samples are quite sparse. This can cause issues with scanning because of trying to focus on empty fields. Our experimental new software (v3-alpha3) can deal with that issue, but will then not scan beyond any blank fields that it finds.
Thank you very much for the quick reply!
Some coverslips are off-center, so that might be an issue but maybe I’ll figure something out to keep them on once I make the microscope. Worst case, we’ll just make additional slides that are centered.
I’ll probably try out scanning with 40x at first, just to see the results (some virtual slides at that magnification look really good, despite diatoms requiring 60x or above). If high magnification is needed, instead of scanning the whole thing, will find a smaller area that’s most abundant to not have to capture so many images. Having partial scans might also be fine, as long as we have enough cells to count. The software also sounds very promising!
Thank you for helping me make a decision! I’ll post on the forum my results.