Description: after segmenting with Omnipose and continuing in MATLAB, this error appears along with errors in ssoSegFunPerReg, doSeg, intProcessXY, BatchSuperSeggerOpti, processExp
Explanation: Supersegger-Omnipose is not able to find the masks because one of the folders containing your dataset is named 'seg'.
Fix: change the name of the 'seg' folder (ex. 'seg1') and retry (no need to delete existing folders)
Description: when making a cell kymograph mosaic through superSeggerViewerGui, the output is 2 of the same mosaic figures and 1 empty figure.
Explanation: There is a bug.
Fix: Ignore the extra figures.
Description: when making a cell movie through superSeggerViewerGui, the movie is not made and there is an error.
Explanation: The frame size generated by makeCellMovie is able to change, while saving a movie with MATLAB's writemovie requires all frames of the movie to be the same size.
Fix: In progress; try to manually create the movie using makeCellMovie.m
Description: when making a cell kymograph mosaic for 1 or more specific cells through superSeggerViewerGui by inputting the cell numbers, there is an error.
Explanation: There is probably a bug; also not sure if the function allows for these input parameters (may only allow Max Cells argument rather than specific cell numbers).
Fix: Manually create the kymographs individually using Cell Kymo in the ViewerGui, or makeKymographC.m
Description: when installing the stable version of Omnipose (pip install omnipose), there is an error with the library
Explanation: Not sure what causes this error.
Fix: Reinstall numpy first (pip install numpy), then rerun pip install omnipose.