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nygctech / hudson

Pyseq 4i spatial pipeline
GNU General Public License v3.0
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preview images that are gamma & contrast corrected, maybe also cropped #30

Closed krpandit closed 1 month ago

krpandit commented 1 month ago

updated pyseq-image to use class methods to open different types of image from tiffs, xarray created zarr, ome-zarr created zarr, pyseq RoughFocus, and pyseq ObjStack

To use: im = HiSeqImages.open_tiffs(PATH) im = HiSeqImages.open_zarr(PATH) # will work for xarray of ome-zarr created zarr

Added tests for opening from tiffs, xarray created zarr, ome-zarr.

Also create new function to create preview images from 5D images that have channel and cycle dimensions or 4D images with a marker dimension, along with a test for the 5D case.

TODO:

krpandit commented 1 month ago

updated get_HiSeqImages in pyseq-image to use classmethods to open tiffs or zarr so we don't have to update the snakemake files.

see commit 39bb50c41c384f4282f814a10f2ef0ca514ed416 in the pyseq-image preview branch

krpandit commented 1 month ago

I updated unmix, picasso, and pyseq-image, environments to use pyseq-image updated with class methods to open files.

The picasso script was updated to use pyseq-image to open zarr file and old commented out code was deleted.

I found a bug in the segmentation script when using both a nuclei and cytoplasm image. The cytoplasm and nuclei channel index was [1,2] respectively but it was changed to [0,1].

The unmix script was updated to use the new pyseq-image class methods to open zarr file from processed zarr and then save ome-zarrs. Also added code to write preview images, and added a section specific preview directory to the output of the unmix snakemake rule. I also deleted old commented out code.

krpandit commented 1 month ago

merged preview branch with main without any errors, deleted preview branch, closing this issue.