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liangyou03
/

SPInfer-ROSMAP

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Image Segmentation

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SPInfer-ROSMAP / README.md

liangyou03

Replace dataset with one-level categorized brain_data release

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metadata

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

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:

README.md
manifest.tsv
dataset_metadata.json
00header.txt
.gitattributes

Files pair by stem. For example:

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:

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.