Add image segmentation docs #1821
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…bility.py to accept variable data_set names.
Co-Authored-By: Tony Tung <[email protected]>
| a few methods that are implemented or integrated with starfish to output a | ||
| :py:class:`.BinaryMaskCollection`, which represents a collection of labeled objects. If you do not | ||
| know which segmentation method to use, a safe bet is to start with thresholding and watershed. On | ||
| the other hand, if you can afford to manually define ROI masks there is no better way to |
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is ROI common enough parlance that it's not necessary to define it?
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Good point, I will add an entry for ROI in the glossary and link to it.
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| The most accurate but time-consuming approach is to manually segment images using a tool such as | ||
| `ROI manager <https://imagej.net/docs/guide/146-30.html#fig:The-ROI-Manager>`_ in FIJI (ImageJ). It | ||
| is a straightforward process that starfish supports by allowing ROI set binaries to be imported as a |
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"ROI set binaries" is confusing to me. Do you mean ROI sets saved as binary files?
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Yes that's what I meant... I got the language from some ROI manager documentation I can't find now but I agree it's confusing. How about "that starfish supports by importing ROI sets stored in ZIP archives".
Co-Authored-By: Tony Tung <[email protected]>
Co-Authored-By: Tony Tung <[email protected]>
Co-Authored-By: Tony Tung <[email protected]>
Co-Authored-By: Tony Tung <[email protected]>
Codecov Report
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Coverage 90.04% 90.04%
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Files 254 254
Lines 9451 9451
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Hits 8510 8510
Misses 941 941Continue to review full report at Codecov.
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Added tutorials for watershed, manual, and ilastik segmentation in starfish. Also made minor edits to
from_fiji_roi_setsdocstring and changedIlastikPretrainedProbabilityto clarify how to use in Windows and accept variable dataset names that are exported from ilastik.link to readthedocs