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AdvancedImagingUTSW opened this issue Aug 5, 2023 · 0 comments
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enhancement New feature or request

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@AdvancedImagingUTSW
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Currently, we have a volume search feature that is working nicely. I do not want to change this feature, but rather, build another feature that is the next logical step.

As implemented, the volume search feature images the tissue at low resolution at one position in X and Y, and finds its boundaries in Z. The boundaries are then automatically identified, we switch resolution, and then image the tissue automatically at a higher magnification by moving it in X, Y, and Z. However, if regions of the tissue go beyond what is in the field of view of the low resolution system, we do not image those. And importantly, most of our microscopes do not have multiple resolution modes, so we cannot take advantage of this functionality.

The next iteration of the feature should be designed to operate with the microscopes that are not multi-scale. We should ideally be able to put a tissue into the microscope, get the specimen to a location where it can be detected, and hit go. There are multiple ways that we could implement this... In the first format, we could sample the 3D volume at different intervals to see where the tissue is, then build up a sequence of multi position acquisitions to image it all. We previously discussed an octree-based approach for finding the tissue in an efficient fashion. Or, we could go into a while loop like format that images in each Z direction until the sample is no longer detected, then moves in X or Y, and repeats.

Stage limits are exceedingly important for such a system, since that is our only mechanism for preventing crashes.

@annie-xd-wang, feel like something you would want to implement?

@AdvancedImagingUTSW AdvancedImagingUTSW added the enhancement New feature or request label Aug 5, 2023
@AdvancedImagingUTSW AdvancedImagingUTSW changed the title Second Iteration of Volume Search Feature New Feature - Second Iteration of Volume Search Feature Aug 6, 2023
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