Add Widefield segmentation data for blue and violet channels

[weiglszonja]

Add segmentation data for the Widefield imaging session

• PlaneSegmentationProcessedBlue contains the ROIs (centroids and labels) and the image_masks for the downsampled imaging (blue channel) links to ImagingPlaneBlue
• SegmentationImagesBlue contains the manual mask and the contrast based vasculature mask for the blue channel in the full size session image. (1024 x 1024)
• SegmentationImagesProcessedBlue contains the contrast based vasculature and the pca mask for the blue channel in the binned image. (128 x 128)
• SegmentationImagesProcessedViolet contains the pca mask for the violet channel in the binned image. (128 x 128)

[weiglszonja]

Stub file on s3 is at pinto-lab-to-nwb/new_stub_DrChicken_20230419_20hz.nwb

[CodyCBakerPhD]

Everything looks good except for the processed 1P series (in discussion, not sure why this was getting set in this way) is currently float64 but should be uint16? Possibly something to do with how the numpy array is pre-allocated?

[weiglszonja]

@CodyCBakerPhD
For the processed 1P, the dtype of video is determined from the dtype from DatasetView as we read the mat file in, which is float64

self._video = DatasetView(file[expected_struct_name])

But I also checked for the raw 1P, and that should be float16 which is float64 right now, but that should be an easy fix in roiextractors (and this one is because of creating a pre-allocated array without specifying the data type, which defaults to float64): catalystneuro/roiextractors#257

[CodyCBakerPhD]

@weiglszonja OK let me know when there's a new file to check and this should be good

[weiglszonja]

@CodyCBakerPhD Thanks, this change should be reflected at new_stub_DrChicken_20230419_20hz.nwb

[CodyCBakerPhD]

@weiglszonja It looks like the same neurodata objects still have the same float64 data type in the new file

[weiglszonja]

For the raw they show up as uint16 for me as here:

updated: stub_DrChicken_20230419_20hz.nwb

[CodyCBakerPhD]

@weiglszonja Sorry for not being clear with which data set I'm talking about

[weiglszonja]

TODO:
as per our meeting add dtype at init for processed imaging interface, which will either keep the float64 if they request or cast it to int16 by default

[weiglszonja]

updated file: DrChicken_20230419_20hz.nwb

[CodyCBakerPhD]

Yep, that looks great now!