README.md

---
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.