hjmh / fly2p Goto Github PK
View Code? Open in Web Editor NEWutility functions for analyzing (fly) calcium imaging data
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fly2p's Issues
implement saving/storing of shapely rois (used in EB imaging analysis) in metadata
Need to decide on a convenient format for describing these rois and then implement saving them as part of the imagingTimeseries dataclass.
add background subtraction to DFF function
This could be optional in computeDFF and the region used for computing the background should be passes as a mask.
fix saving/loading of multidimensional xarrays
xarrays appear to not be saved properly to file
I use to_netcdf to save the arrays (F0stack.to_netcdf(sep.join([savepath,'F0stack.nc'])) ) and was planning to load them using open_dataset (xr.open_dataset(path2imgdat+sep+'F0stack.nc') ).
It's been a while since I debugged this, so further investigation is necessary.
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