Diatom arranging station + 4k video stack examples

[Beatsy]

Some time ago, I got fed up of taking manipulators off my main scopes when I needed them for something else, then having to set the manipulators up again when I switched back to diatom arranging. It became quite a barrier to both pursuits in practice. I found myself spending far more time on studio macro instead (another desk space hog) with diatom arranging just "ticking over" and photomicrography pretty much dormant. So I decided to get extra kit to make a separate setup for diatom arranging, but studio macro had me proper distracted and a year flew by with the accumulating diatom gear still awaiting deployment. Anyway, at last, I have a dedicated diatom arranging station on a sturdy table of it's own. Yaayyy! It's a Nikon Labophot with epi objectives plus transmitted and epi illumination coupled with a hydraulic micro-manipulator. I also use a Nikon stereo (not shown) but that lives in its box until needed as the Labophot supports nearly every aspect of arranging on its own (more than I expected).

When searching strews in the past I made it a habit to immediately photograph rare and interesting forms on my Zeiss inverted (the forms were still open to the air on large coverslips at that point). This allowed me to get multiple views of a single specimen (not possible once mounted) and offered insurance against them being pinged into the blue yonder during subsequent arranging. I had intended to continue this practice on the Zeiss, but the Labophot came with a photo port so I figured I may as well use that instead.

To that end, I revisted stacking using 4k video frames. I've posted some bugs done this way before, but I don't think I've ever posted any diatoms done in 4k (I have used HD video stacking for them and posted about that though). Thing is, the Labophot has a more sensible image scale due to its 2.5x relay lens compared to the Zeiss ICM 405 and it's built in 3.2x. So when using 4k video, the Labophot produces better images with less empty magnification. I'm really pleased with the test results, especially considering how quick and trivially easy they were to do. First two test images attached (technical details next to the pictures).

Despite thoroughly enjoying the intervening distractions it's great to get back to "serious diatoms" again. And my studio macro setup keeps its dedicated work area so I'll carry on with that too. Contentment restored


My new, dedicated "diatom arranging station"


Brightfield. Nikon M-Plan 20/0.4 + 2.5x relay lens. 100 images from 4k video, pmax stacked. Cropped and levels adjusted. Brightfield.


Brightfield. Nikon M-Plan 40/0.65 + 2.5x relay lens. 130 images from 4k video, pmax stacked. Cropped and levels adjusted.

[zzffnn]

Very nice, Beatsy!

So when you do 4k video stacking:

1) do you manually turn fine focus, at a constant pace, from top focus plane to bottom focus plane?

2) what frame rate per second do you use for say NA 0.4 objective vs NA 0.6 objective? Does it matter?

Thank you for sharing!

[Beatsy]

Very nice, Beatsy!

So when you do 4k video stacking:

1) do you manually turn fine focus, at a constant pace, from top focus plane to bottom focus plane?

2) what frame rate per second do you use for say NA 0.4 objective vs NA 0.6 objective? Does it matter?

Thank you for sharing!

Thanks
1. Yes
2. My camera's 30fps in 4k, but 24fps is OK too. Just wind the fine focus slowly and as evenly as possible. You get a feel for the right speed after a while. Higher NA needs smaller focus steps (step-size*30 is max distance to move focus per second - but move closer to half that speed to be sure to overlap in-focus regions in adjacent frames). Too fast will be obvious due to OOF gaps in the stack. Too slow, or uneven doesn't seem to cause problems (apart from taking longer than necessary to process).