Two bits of software for microscopists with cameras
One of the recurrent issues I have when trying to photography informative characters in small organisms is capturing in an image the level of detail I can see with my eyes. With the twirl of the stage knobs and the focus knobs and the diaphragm, I can see leaves from base to tip through different cell layers with the required levels of light. But when you take a photograph, you only capture one frame in one plane.
Modern microscopy imaging setups have been able to deal with this issue with automated stacking and tiling that is integrated with the camera and its requisite software. For the homebrew microscopists, it gets a little trickier absent a very expensive microscope. To that end, i've recently discovered a great peice of cross-platform open-source software called "Hugin". While its meant for home-stitching of panoramas from image sequences, it is actually amazing for stitching together microscope photos. Not only does it stitch together in the X & Y planes, it also can do a version of focus stacking by stiching between optimal sections of each photo. This has allowed me to shoot entire leaves in focus, both in surface veiw and in cross section. I've pasted a recent observation of Pogonatum contortum as an example.
Another tool that I have found useful for about 20 years now is ImageJ. Developed by the US NIH for analytical tasks generally related to cell imaging, it has a deep library of plugins and add ons that make it very helpful. I use it to measure things like cell dimensions, variation in spore size, surface area of leaves and other tasks that used to take way more work. It has a focus stacking module that is ideal for imaging spores. @david1945wagner has an incredible PDF linked at his website that goes through lots of tips and tricks for home microscopy. Amongst them is the construction of a a tool to standardize increments through the focus plane to make for optimum results when you feed them into stacking software.
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rambryumDescripción
Growing on bank of glacial till.
(A) Habitat (B) Population scale habit showing gametophytes and sporophytes. (C) Young gametophyte. (D) Older gametophyte showing large teeth and thin lamina at margins. (E) Round capsule showing hairy calyptra ensheathing rostrate operculum. (F) Micrograph showing peristome teeth. (G) Transverse section of leaf showing anatomy and short lamellae topped by round, unornamented terminal cells. (H) Whole mount of leaf showing large teeth and numerous rows of lamellae. (I) Transverse section through whole leaf showing lamellae in profile.
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The only thing missing from these excellent photos is a scale embedded in the final image. This is not difficult and is very important when comparing cell structure and size among species. The critical step in the process is to remember to take a picture of a stage micrometer for every photomicrograph session, one for each objective used in that session. That will be used to calibrate a suitable scale template to use in the final photos. A scale with micrometer increments is much better than a scale bar.
Here is an example of a simple scale, fine for recording cell size ( Nardia scalaris ),
https://herbarium.science.oregonstate.edu/wagner/liverworts/livimage/junrub06.jpg
Often a more precise scale is useful for measuring oil body size as well as cell size (
Gymnocolea inflata):
https://herbarium.science.oregonstate.edu/wagner/liverworts/livimage/gyminf08.jpg
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