Datasets:
| 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: <stem>.tiff | |
| marker/ matched marker channel images: <stem>_marker.tiff | |
| cellbodies/ manual cell-body instance annotations: <stem>_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. | |