Datasetpublic

liangyou03/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… See the full description on the dataset page: https://huggingface.co/datasets/liangyou03/SPInfer-ROSMAP.

sourceHugging Facecc-by-4.0updated 4mo agoView on Hugging Face

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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.