Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
A bugfix for the condition when a 3D SBX with 3 or 4 planes is converted to TIF. By default, tifffile assumes the 4th dimension is the color channel, so it is necessary to set photometric to MINISBLACK to avoid each plane being 3-dimensional.
An added feature, the plane argument to SBX loading/conversion functions, which allows extraction of a single plane without keeping the singleton dimension. This is useful when opting to process each plane of a volumetric dataset individually.
Type of change
Please delete options that are not relevant.
[x] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
Has your PR been tested?
If you're fixing a bug or introducing a new feature it is recommended you run the tests by typing
Yes, caimanmanager test passes and new tests have been added for both of these changes.
pgunn
commented
7 months ago
Description
This PR includes two changes:
photometrictoMINISBLACKto avoid each plane being 3-dimensional.planeargument to SBX loading/conversion functions, which allows extraction of a single plane without keeping the singleton dimension. This is useful when opting to process each plane of a volumetric dataset individually.Type of change
Please delete options that are not relevant.
Has your PR been tested?
If you're fixing a bug or introducing a new feature it is recommended you run the tests by typing
Yes,
caimanmanager testpasses and new tests have been added for both of these changes.