Replace dataset with one-level categorized brain_data release: remove previous files

00header.txt

@@ -1,421 +0,0 @@
-gfap_3527_cellbodies.npy
-gfap_3527_marker.tiff
-gfap_3527.tiff
-gfap_3532_cellbodies.npy
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-gfap_3532.tiff
-gfap_3569_cellbodies.npy
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-gfap_4238.tiff
-gfap_4319_cellbodies.npy
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README.md

@@ -1,52 +0,0 @@
----
-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.
-
-## Contents
-
-- `<stem>.tiff`: DAPI channel image.
-- `<stem>_marker.tiff`: matched marker channel image.
-- `<stem>_cellbodies.npy`: manual cell-body instance annotation.
-- `<stem>_dapimultimask.npy`: manual DAPI/nucleus instance annotation for the annotated subset.
-- `00header.txt`: file list from the local source folder.
-- `manifest.tsv`: file sizes and SHA256 checksums.
-- `dataset_metadata.json`: file counts and naming metadata used for staging.
-
-The dataset is intentionally stored as a flat folder. Stems encode marker family and tile id, for example:
-
-```text
-gfap_5789.tiff
-gfap_5789_marker.tiff
-gfap_5789_cellbodies.npy
-gfap_5789_dapimultimask.npy
-```
-
-Clinical/pathology tables are not included.
-
-## 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.

dataset_metadata.json

@@ -1,23 +0,0 @@
-{
-  "repo_id": "liangyou03/SPInfer-ROSMAP",
-  "source": "data/brain_data",
-  "layout": "flat brain_data folder",
-  "counts": {
-    "dapi_tiff": 120,
-    "marker_tiff": 120,
-    "cellbodies_npy": 120,
-    "dapimultimask_npy": 30,
-    "other": 1
-  },
-  "naming": {
-    "<stem>.tiff": "DAPI channel image",
-    "<stem>_marker.tiff": "marker channel image",
-    "<stem>_cellbodies.npy": "manual cell-body instance annotation",
-    "<stem>_dapimultimask.npy": "manual DAPI/nucleus instance annotation"
-  },
-  "notes": [
-    "Clinical/pathology tables are excluded.",
-    ".ipynb_checkpoints and local cache files are excluded.",
-    "The public dataset release intentionally avoids nested raw_annotations/cellpose_prepared/metadata folders."
-  ]
-}

gfap_3527_cellbodies.npy

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:b5ab4b9fb021f4fb1be1ef4af96a6d33d5cf36c4e99f96f6597e8c092ece7d96
-size 2887168

gfap_3532_cellbodies.npy

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:3b90214718f3e954a1e270d5783692de9ee147efb7d38253b98e85f4d68529fa
-size 2887168

gfap_3569_cellbodies.npy

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-oid sha256:7ad763b00d736f997147e4a7691f211ee98091561894023455ab7cb7c28a7a60
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gfap_3999_cellbodies.npy

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-oid sha256:8f28b9dc4a230628ecdcadbbbbc623d5146f9fc2a2383273e4c69160697a6fc9
-size 2887168

gfap_4201_cellbodies.npy

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-oid sha256:fa17d2978bf708dc0f409d701d7b62a9593dc0fe326849e614f5b176154e1655
-size 2887168

gfap_4201_dapimultimask.npy

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-oid sha256:06c6694c58406bbbed117bf9e66c2ab4fd87f0d77dd87d2fcc4c231b1147280d
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gfap_4238_cellbodies.npy

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gfap_4319_cellbodies.npy

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gfap_4515_cellbodies.npy

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gfap_4548_cellbodies.npy

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gfap_4642_cellbodies.npy

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gfap_4683_cellbodies.npy

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gfap_4736_cellbodies.npy

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gfap_5059_cellbodies.npy

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-size 2887168

gfap_5191_cellbodies.npy

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gfap_5410_cellbodies.npy

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