Automated Slide Scanning and Tiling

General
13

@evolk, I have not got detailed answers on @JohemianKnapsody’s code, but there are some other questions in there as well.

  1. The units are steps of the small stepping motors (about 4000 steps per turn of the small gear). The easiest way to tell how many steps you need to move in a scan is to use the navigate tab to move the sample manually and see how many steps it is to go across the whole image in x and y. For good stitching I think you need to aim for at least 1/3 image overlap.
    The camera stage mapping also saves a calibration file that tells you how many steps per pixel of the image.
    If you are needing to focus through the thickness of a microscope slide (about 1mm) then it is usually possible to manage with most x20 objectives, although they are not designed to give the best images with a thick glass. There are x20 and x40 objectives that are specifically designed for this purpose, labelled 160/1.1 or (infinity)/1.1. For example CCIS® Plan achromatic objective LWD PL 40X/0.5 (WD=3.0mm) (there is also a 20x). I am sure someone posted a similar one from Amscope, but I cannot find it just now(edit: not Amscope Is this the correct specs for a LM objective? - #5 by heehaw). You will need the correct optics module for your microscope to match the standard (160/) or infinity corrected objective.

  2. In a scan the consecutive images are close together, so it should be able to find the focus when it moves to the next tile. If there is a large move between images - as in a raster scan going to the next line - then there can be issues. A snake or spiral scan never makes long moves. @JohemianKnapsody is making progress on predictive focus - based on the images in the current scan and / or the known stage geometry. I don’t know how much of that is in the code linked here. We are at a change-over in the software from v2 to v3, some new features are not compatible with v2, but v3 is not ready for an alpha release.
    Note that the scan size in xy is not clear for a spiral scan. If you select spiral then the number of y-steps is ignored. the number of x-steps is used as the number of spiral rings, I think. There is a thread on the Forum on the pattern for spiral scans, I think.

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