Annotate/Classify example data: 2341 crops, 88 labels, portable paths

.gitattributes

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 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+measurements.db filter=lfs diff=lfs merge=lfs -text

README.md

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+---
+license: mit
+task_categories:
+  - image-classification
+tags:
+  - spacr
+  - microscopy
+  - annotation
+  - toxoplasma
+pretty_name: spaCR Annotate and Classify example data
+---
+
+# spaCR — Annotate and Classify example data
+
+Example input for the **Annotate** and **Classify** modules of
+[spaCR](https://github.com/EinarOlafsson/spacr). It is the output of a Measure
+run, so both modules can be exercised without segmenting or measuring anything
+first.
+
+## What is here
+
+| Path | What it is |
+|---|---|
+| `data/` | 2,341 single-cell PNG crops, foldered by phenotype |
+| `measurements.db` | The measurements, plus `png_list` and the annotation tables |
+| `measurements/active_learning/` | The model card from the first annotation round |
+| `settings/annotate_settings.csv` | Settings for the Annotate module |
+| `settings/classify_settings.csv` | Settings for the Classify module |
+
+## It carries real annotations
+
+`png_list.annotate` holds **88 labels** — 50 of class 1 and 38 of class 2 —
+against 2,253 unlabelled crops, with 101 rows of per-round history in
+`annotation_rounds`. That is what makes this usable as a *classify* set: a
+training example needs labels, and unlabelled crops alone would only exercise
+the viewer.
+
+The first active-learning round is recorded too: 88 labels, 25 held out by
+well, `holdout_accuracy` 1.0 on a `StratifiedGroupKFold` split where no well
+appears on both sides. Treat that number as a demonstration of the workflow,
+not as a result — 88 labels over four wells is a very small set.
+
+## Paths are RELATIVE, deliberately
+
+Every path in `measurements.db` and in both settings files is relative to the
+dataset root:
+
+```
+data/single_nucleus/uninfected/plate1_E01/cell_png/plate1_E01_19_1_12.png
+```
+
+A measurements database normally stores absolute paths, which name the machine
+that made it and resolve nowhere else. spaCR's downloader rewrites these to
+absolute on arrival, so the database works wherever it is unpacked. If you
+unpack it by hand, do the same, or point spaCR at the folder and let it.
+
+`<dataset>` in the settings files is a placeholder for the unpack location and
+is substituted the same way.
+
+## Plate layout
+
+Four wells (E01, E02, L01, L02) from the plate published as
+[`einarolafsson/spacr-example-measure`](https://huggingface.co/datasets/einarolafsson/spacr-example-measure),
+which holds the merged arrays these crops were cut from.
+
+## Provenance
+
+Produced by spaCR's Mask module and then its Measure module, from spaCR's own
+example images, with `cpsam` for cells and nuclei and a Toxoplasma-specific
+CPSAM checkpoint for pathogens. One field of fifty-two (`plate1_E02_20_1`)
+failed to measure — a nucleus label spanning two cells — so the crops come from
+51 fields. Absolute paths have been rewritten to relative throughout.

data/multiple_nucleus/multiple_pathogens/plate1_E01/cell_png/.spacr_crop_format.json

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+{
+  "channel_order": "declared_rgb",
+  "narrowing": "high-byte",
+  "note": "The red, green and blue channels hold the source channels named by settings['png_channel_mapping']. No list-position convention is involved, so there is nothing here to read backwards.",
+  "spacr_crop_format": 3,
+  "updated_utc": "2026-09-01T18:48:32Z"
+}

data/multiple_nucleus/multiple_pathogens/plate1_E02/cell_png/.spacr_crop_format.json

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+{
+  "channel_order": "declared_rgb",
+  "narrowing": "high-byte",
+  "note": "The red, green and blue channels hold the source channels named by settings['png_channel_mapping']. No list-position convention is involved, so there is nothing here to read backwards.",
+  "spacr_crop_format": 3,
+  "updated_utc": "2026-09-01T18:48:28Z"
+}

data/multiple_nucleus/multiple_pathogens/plate1_L01/cell_png/.spacr_crop_format.json

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+{
+  "channel_order": "declared_rgb",
+  "narrowing": "high-byte",
+  "note": "The red, green and blue channels hold the source channels named by settings['png_channel_mapping']. No list-position convention is involved, so there is nothing here to read backwards.",
+  "spacr_crop_format": 3,
+  "updated_utc": "2026-09-01T18:48:18Z"
+}