I am trying to work out what the best way to capture some stacks under the microscope is. I currently have a stepper motor on the Z-Axis which works great, however I like the idea of video captures as a way to avoid killing the shutter very quickly.
My next step is to look towards automating the X/Y axis and my thought was if I was trying to capture a large item, I could tell it to start top left, working to bottom right and capturing a Z axis Video for each X/Y position. The issue is though around how Helicon Focus might actually handle these images, for example if there is no focus will it not do anything, secondly and more important, since a lot of the item might be differing thicknesses would Helicon focus work on a video where the upper and lower limits are specified but it may not all be in focus (e.g. it extends past the upper focus point).
Is there the capacity in batch mode (once video is supported) to 'throw' away frames which don't contribute any sharpness to the overall image?
Optical microscopes + digital photography
Moderator: Stas Yatsenko
The unfocused images may or may not break the final result. As a rule of thumb, it's best to remove them from the stack manually. In your case I only expect such unfocused images in 2 contiguous chunk in the beginning and the end of the stack, so removing them shouldn't take long.