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janelia-cellmap / cellmap-nuclei

Generating nucleus segmentations for FIB-SEM datasets of cells and tissues
BSD 3-Clause "New" or "Revised" License
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jrc_mus-granule-neurons-2 #20

Open jonesa3 opened 3 months ago

jonesa3 commented 3 months ago

used s2 (128nm seemed too low for this dataset)

jonesa3 commented 2 months ago

proofread tif found here: /avetissiane/tiff_slices/jrc_mus-granule-neurons-2/s2_cp_masks_amira_proofread.tif

jonesa3 commented 2 months ago

connected components proofread tif found here: /avetissiane/tiff_slices/jrc_mus-granule-neurons-2/s2_cp_masks_amira_proofread_cc.tif

yuriyzubov commented 2 months ago

/avetissiane/tiff_slices/jrc_mus-granule-neurons-2/s2_cp_masks_amira_proofread_cc.zarr

yuriyzubov commented 2 months ago

jrc_mus-granule-neurons-2.zarr/recon-2/labels/inference/segmentations/nuc

rinva commented 2 months ago

Image

Thumbnail created.

nrs/data/jrc_mus-granule-neurons-2/thumbnail_nuc.jpg

rinva commented 1 month ago

DOIs created model - https://doi.org/10.25378/janelia.26506327 https://figshare.com/s/797ae268c99e05d20f82 refined segmentations - https://doi.org/10.25378/janelia.26506513 https://figshare.com/s/cc70f4a52d84e8da4159

rinva commented 1 month ago

Ready for meshes.