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I selected the "macro" flair because it's what we have, but in the past two years I've found my interest really lays in "micro". I have two microscopes now. One is a trinocular 10X-40X continuous zoom, and the other is a straightforward Swift 960. It's a high school classic, cheap and effective. With the trinocular scope I'm mounting my camera directly, so the magnification I get is approximately halved from that which I'd see through the eyepieces. With the Swift I'm doing eyepiece projection using a little adapter I picked up on Ebay that clamps onto the microscope eyepiece.
For stacking applications I fluctuate between preferring Helicon and Zerene, and sometimes I use Picolay. I've found the different stacking applications produce quite different results even with similar settings, and some are better for some subjects than others, depending on their characteristics.
I'm interested in chatting with other people who have similar interests or use cases, to compare notes and techniques, to share any little tricks we've picked up, that kind of thing.
My general process: I arrange my subject on the stage, and compose my shot in Live View, and then I turn off Live View because it's a redundant battery drain for me at this stage. It was useful when I was just starting. I use my IR remote to control the shutter release with my left hand, and I increment the fine focus wheel on the microscope with right. I keep my camera set to display a 1 second review so that I can tell when I'm done my stack, but aside from glancing at it periodically I don't watch the screen. I watch my focusing wheel.
I've found I have much better muscle control while looking at the wheel, so I can increment it more evenly and with greater fineness. In this way I'm now shooting manual stacks in excess of 1200 exposures, but only occasionally and for subjects that have a great deal of depth to cover. Most of my stacks are in the 300-600 exposure range, and this proves adequate for most of my subjects. I've found that more isn't always better, too. Sometimes I'll shoot a stack of 600, and then in my stacker I'll select every other image instead of each, and sometimes this produces a better result. The wasted frames are no waste at all, because overall, I do better with consistent focusing adjustments when they're in small increments. If I shoot the same stack but only take 300 exposures, they won't be as evenly distributed in depth.
I have so much fun with this it's almost obscene. I trance out and think wonderful, unfamiliar things while shooting stacks. It's almost meditative, and I try to leverage this to think about the subjects of my writing. My photography and writing are beginning to fuse. My photography is a tool of personal philosophy. This is my motivation to take pictures. I'm digressing, and that should be in a different thread.
In post, I generally import all of my raws into LR, and then I remove the dust because my camera was ancient and well loved, but I didn't keep up with purchasing sensor swabs. LR makes it painless. I only need mask one image, then I can copy the settings and apply them to the stack as a whole. I then select a frame somewhere in the stack that shows the most prominent part of the subject in clear focus, so if I were shooting an insect eye, I'd select a frame perhaps halfway through that shows a thin band of eye cells in focus. I apply some basic adjustments, and then I "copy development settings" and apply them to the entire stack. Finally, I export them to tiff. More recently I've been experimenting with exporting to jpeg with good results, but I do like the tiff format despite its bulk.
When the export is completed I open my stacker, add the images and let it do its thing. I usually restack the same set a few times with different settings. Sometimes I apply retouching from one result to another. I need to improve at this.
After saving the stacker outputs I open up PS and finish making whatever adjustments I feel. I like the Nik plugins a lot, but I'm looking to expand my arsenal. I'm always interested in new sharpening plugins, especially. Of the Nik plugins, the filters I find most useful are Tonal Contrast, Detail Extractor, Dark Contrasts, and White Neutralizer. I think the latter is spectacular for removing faint colour casts and fixing up imperfect white balance.
Important disclaimer: I really have no idea what I'm doing. I learn by feel and trial and error, and I base my idea of success on how I like the results. That's not to say I don't read, I love to read, but I prefer to do, first, where feasible. I just try stuff until I find what works for me, so I'm probably making all kinds of mistakes, and perhaps offering poor advice (particularly about post processing). This is why I'm posting this. I feel by sharing what I think I know, I can learn more from any of you in your responses. I've watched my work improve dramatically over the past two years, and I want to keep furthering all aspects of it.
So, if you're out there, and you do this stuff, please consider sharing what you know. If you want to get started I'm happy to help answer anything I can, with the above disclaimer. Microscopes are amazing for photography. I think they're underused. If you're considering it, do not let it feel daunting due to unfamiliarity. They're simple optical devices, and they can outlive your best lenses by decades. There's so much stuff out there we just can't see any other way, and I find that particularly compelling.
Stay safe all.