Add support for importing different ROIs from ImageJ

kushalkolar / MESmerize

Platform for Calcium Imaging analysis. DEPRECATED.

GNU General Public License v3.0

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Add support for importing different ROIs from ImageJ #68

Closed pr4deepr closed 2 years ago

pr4deepr commented 2 years ago

MESmerize wouldn't import oval, rectangle or freehand ROIs exported via ImageJ. It only accepted polygon ROIs.

Added classmethod from_ellipse for ManualROI class for reading elliptical ROIs
Altered import_from_imagejfunction to accept rectangle and freehand ROIs

Redoing a previous pull request that I closed as it got a bit.... messy: https://github.com/kushalkolar/MESmerize/pull/64

kushalkolar commented 2 years ago

Looks good, thanks for creating a clean new PR! The one last thing I'd do is add a note to the ImageJ line of the table for the ROI Manager UI Controls stating that freehand ROIs are downsampled by 5. It's line 47 in this file:

MESmerize/docs/source/user_guides/viewer/modules/roi_manager.rst

Thanks a lot for your contribution!

pr4deepr commented 2 years ago

Done. Yea, previous one got too messy. Windows kept modifying spectral.png file for some reason. Thanks for your help with this. Happy to keep contributing. Its a great piece of software!

kushalkolar commented 2 years ago

Thanks! Last question, I'm assuming you've tested the new functionality? And old functionality isn't broken.

pr4deepr commented 2 years ago

I'm attaching an ROI file I tested RoiSet.zip When importing this ROI file, I get: It has two freehand ROIs, so takes a few seconds to load.

With old functionality, I can view timeseries traces from an image using freehand rois & import it in the flowchart . Don't think I've broken anything.

kushalkolar commented 2 years ago

Thanks! Merging.