By checking "Align each frame against first frame separately" in Preferences, all frames line up. To clarify... For normal focus stacking, you'll get equal or better results by leaving that option at its default setting, which is not checked. The option is provided for high precision measurement ta...

This last image is a significant improvement in the light.

I notice that the image is posted in "Nature Photography", but with 1300 frames I am thinking it should be in "Technical & Studio Photography". I will move it after you've had a chance to see this comment.

--Rik

Brad, Thank you for the further information. The possibility of softening due to subject movement had not occurred to me. In normal circumstances, all the stacking programs will automatically correct for simple shifts across the frame. However, if the subject does not sit in a stable position, or if...

Welcome to the world of high mag stacking! For background and disclosure, I'm the fellow who wrote Zerene Stacker. I also answer all of its email requests for support. So, my comments here will be from the background of having helped hundreds of other people in that role, in addition to my postings ...

Thanks for including the original. That matches pretty close to what I got by inverting the lightness channel in an Lab version of your post at top of thread. But it does not match exactly, so now I am curious. I notice that in your original, the eyes are very dark, almost black. With inverted lumin...

Excellent -- and that is a very clever trick, to invert just the luminosity channel so as to convert brightfield to darkfield while preserving colors!

--Rik

With regards to focus blocks, the well regarded Olympus BHMJ is actually quite expensive. Would something much cheaper (e.g. https://www.ebay.com/itm/Stereo-Microscope-Adjustment-Coaxial-Coarse-and-Fine-Focusing-Arm-E-Head-Holder/273448954661) be equally suitable/capable? Very interesting! Today's ...

Viewing your image at full resolution (5496 x 3864), I see a lot of lateral chromatic aberration -- color fringes away from center on light vs dark transitions. That is a property of the objective. You can eliminate the obvious fringing with post-processing in Photoshop and similar tools, but fringi...

In CS4, I believe it was File > "Save for Web & Devices", so directly under the File menu, not under Export.

--Rik

What's making your files too large is metadata embedded in them. Get rid of that and there should be no trouble with size. In Photoshop, the simplest approach is to save the image using File > Export > Save for Web (Legacy). Using GIMP, follow the instructions at https://www.makeuseof.com/tag/3-ways...

Thanks for the detail about preparation. About the colors, I have seen Pau's approach used a few times. Doing it fully automatically is indeed tricky because you have to match perspective -- not just viewing angle but also distance from center of perspective to the subject. This requires a careful m...

Thank you for the additional information. These images look great. I like to hear your thoughts on the fuzziness around the hairy portion of the seed. Do you think if that can still be minimized further? If so, how? I assume that by "fuzziness" you refer to areas like I have marked here, where it se...

Great!

Can we see the final image, please? I am very curious what this subject looks like (and what it is, for that matter).

Also it would be great to get some information about magnification, step size, number of frames, and so on.

--Rik

I notice three things that seem relevant: 1. In the right-hand image, the front structure is very high contrast and is surrounded by a discolored edge. This suggests an extreme value of "brightness" adjustment, caused by having some source frames that are very different from other source frames. 2. ...

I have compared DMap interpolated with "Bicubic", "Lanczos2", "Lanczos4" and found no difference. But in general, DMap performance is much better than PMax, regardless of interpolation method. Does it depend on the blue scales or my setup? In general, DMap is better at handling simple geometries th...