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Add spot finding and decoding docs#1825

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mattcai merged 16 commits intomasterspacetx/starfish:masterfrom mcai-spots-docsspacetx/starfish:mcai-spots-docsCopy head branch name to clipboardMar 23, 2020

+1,203-72

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Commits on Feb 21, 2020

• added watershed tutorial and fixed typo in MinDistanceLabel docstring

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Commits on Feb 22, 2020

• had to remove ':py:param:' because it's not recognized by sphinx

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• fixed broken references

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• fix ':term:<auxiliary images>' not in glossary

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Commits on Feb 24, 2020

• completed manual segmentation tutorial

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Commits on Feb 26, 2020

• completed segmentation tutorials and edited ilastik_pre_trained_probability.py to accept variable data_set names.

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• removed 'plot_' prefix and added necessary files

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• Merge remote-tracking branch 'origin/master' into mcai-segmentation-docs

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Commits on Mar 11, 2020

• finished all spot finding and decoding docs

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• undo some changes in notebooks

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• remove plot_ prefix so it can render in readthedocs

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Commits on Mar 12, 2020

• added ROI to glossary and links to it in tutorials

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• Merge branch 'master' into mcai-spots-docs

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Commits on Mar 13, 2020

• Revert some unintended changes.

  

  Tony Tung

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Commits on Mar 16, 2020

• addressed starfish team's comments

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Commits on Mar 20, 2020

• added comparison of spot finding methods and added warnings to spot finding how-tos regarding their compatibility with cropped data sets and their support for 2D slices of a volume

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