diff --git a/00header.txt b/00header.txt new file mode 100644 index 0000000000000000000000000000000000000000..ee9fee7342a8fc4ed98a4e0ae8e03d210577b3c1 --- /dev/null +++ b/00header.txt @@ -0,0 +1,421 @@ +gfap_3527_cellbodies.npy +gfap_3527_marker.tiff +gfap_3527.tiff +gfap_3532_cellbodies.npy +gfap_3532_marker.tiff +gfap_3532.tiff +gfap_3569_cellbodies.npy +gfap_3569_marker.tiff +gfap_3569.tiff +gfap_3999_cellbodies.npy +gfap_3999_marker.tiff +gfap_3999.tiff +gfap_4201_cellbodies.npy +gfap_4201_dapimultimask.npy +gfap_4201_marker.tiff +gfap_4201.tiff +gfap_4238_cellbodies.npy +gfap_4238_marker.tiff +gfap_4238.tiff +gfap_4319_cellbodies.npy +gfap_4319_marker.tiff +gfap_4319.tiff +gfap_4515_cellbodies.npy +gfap_4515_marker.tiff +gfap_4515.tiff +gfap_4548_cellbodies.npy +gfap_4548_marker.tiff +gfap_4548.tiff +gfap_4642_cellbodies.npy +gfap_4642_marker.tiff +gfap_4642.tiff +gfap_4683_cellbodies.npy +gfap_4683_marker.tiff +gfap_4683.tiff +gfap_4736_cellbodies.npy +gfap_4736_marker.tiff 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+olig2_12798_cellbodies.npy +olig2_12798_dapimultimask.npy +olig2_12798_marker.tiff +olig2_12798.tiff +olig2_12799_cellbodies.npy +olig2_12799_marker.tiff +olig2_12799.tiff +olig2_13161_cellbodies.npy +olig2_13161_marker.tiff +olig2_13161.tiff +pecam_15591_cellbodies.npy +pecam_15591_dapimultimask.npy +pecam_15591_marker.tiff +pecam_15591.tiff +pecam_15968_cellbodies.npy +pecam_15968_dapimultimask.npy +pecam_15968_marker.tiff +pecam_15968.tiff +pecam_15969_cellbodies.npy +pecam_15969_dapimultimask.npy +pecam_15969_marker.tiff +pecam_15969.tiff +pecam_15970_cellbodies.npy +pecam_15970_dapimultimask.npy +pecam_15970_marker.tiff +pecam_15970.tiff +pecam_15971_marker.tiff +pecam_15971.tiff +pecam_15972_dapimultimask.npy +pecam_15972_marker.tiff +pecam_15972_roiset_15972_pecam.npy +pecam_15972.tiff +pecam_15973_cellbodies.npy +pecam_15973_dapimultimask.npy +pecam_15973_marker.tiff +pecam_15973.tiff diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..b16ebb97ed6a7f562369fe6f1fdc024f0d298a7f --- /dev/null +++ b/README.md @@ -0,0 +1,68 @@ +--- +license: cc-by-4.0 +task_categories: + - image-segmentation +tags: + - immunofluorescence + - cell-segmentation + - brain +pretty_name: SPInfer ROSMAP +--- + +# SPInfer Brain IF Data + +This repository contains the compact public SPInfer brain immunofluorescence annotation dataset. + +## Layout + +```text +dapi/ DAPI channel images: .tiff +marker/ matched marker channel images: _marker.tiff +cellbodies/ manual cell-body instance annotations: _cellbodies.npy +dapimultimask/ manual DAPI/nucleus instance annotations for the annotated subset +``` + +Root files: + +```text +README.md +manifest.tsv +dataset_metadata.json +00header.txt +.gitattributes +``` + +Files pair by stem. For example: + +```text +dapi/gfap_5789.tiff +marker/gfap_5789_marker.tiff +cellbodies/gfap_5789_cellbodies.npy +dapimultimask/gfap_5789_dapimultimask.npy +``` + +Clinical/pathology tables are not included. + +## File Counts + +- 120 DAPI images +- 120 marker images +- 120 cell-body annotations +- 30 DAPI/nucleus multi-mask annotations + +## Package + +Use with the SPInfer package: + +```bash +spinfer doctor --config configs/paths.yaml +spinfer prepare-cellpose --config configs/paths.yaml +``` + +## Source + +Local staging was prepared for `liangyou03/SPInfer-ROSMAP`. + +## Citation + +Please cite the SPInfer manuscript and software release when using this dataset. diff --git a/cellbodies/gfap_3527_cellbodies.npy b/cellbodies/gfap_3527_cellbodies.npy new file mode 100644 index 0000000000000000000000000000000000000000..023e96fa26430127057cacbe151a84ecbd47a2ec --- /dev/null +++ b/cellbodies/gfap_3527_cellbodies.npy @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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