Add files using upload-large-folder tool

.gitattributes

@@ -58,3 +58,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+aggregated/01_JUMP_DINO_ECFP4_C_aggregated.h5ad filter=lfs diff=lfs merge=lfs -text
+cp_measure/jump_cp_well.h5ad filter=lfs diff=lfs merge=lfs -text

README.md

@@ -1,3 +1,101 @@
----
-license: cc0-1.0
----
+---
+license: cc-by-4.0
+language:
+- en
+pretty_name: cp-bg-bench preview (jump)
+size_categories:
+- 1K<n<10K
+task_categories:
+- image-classification
+tags:
+- cell-painting
+- microscopy
+- biology
+- benchmark
+configs:
+- config_name: crops
+  data_files:
+  - split: train
+    path: crops/data-*.arrow
+- config_name: crops_density
+  data_files:
+  - split: train
+    path: crops_density/data-*.arrow
+- config_name: seg
+  data_files:
+  - split: train
+    path: seg/data-*.arrow
+- config_name: seg_density
+  data_files:
+  - split: train
+    path: seg_density/data-*.arrow
+---
+
+# cp-bg-bench preview — jump
+
+Compact preview of the **jump** dataset from the cp-bg-bench
+benchmark. Stratified subset of the full release; designed so that the
+held-out-batch perturbation-recall and cp_measure-prediction evals can
+be reproduced end-to-end against this small slice alone.
+
+| | |
+|---|---|
+| Cells | 913 |
+| Wells | 69 |
+| Perturbations | 33 |
+| Held-out batch | `source_4` |
+| Views | crops, crops_density, seg, seg_density |
+
+## What's in this repo
+
+```
+crops/                # HF dataset, 224×224×C uint8 cell crops + masks
+crops_density/        # crops + 4 corner density patches
+seg/                  # mask-applied cell crops
+seg_density/          # mask + density patches
+aggregated/           # well-level aggregated h5ad with X_pca + X_pca_harmony
+cp_measure/           # well-level cp_measure features (~1300-1400 features)
+metadata/             # perturbations parquet + quality filter report
+build_info.json       # full provenance (seed, source pipeline commit, selection stats)
+```
+
+## Schema (per cell row)
+
+```
+row_key, source, plate, well, tile, id_local                              # identity
+nuc_area, cyto_area, nuc_cyto_ratio, n_cells_in_fov, n_cells_scaled        # per-cell QC
+mask:  large_binary  # (2, 224, 224) uint8 -> NucMask, CellMask
+cell:  large_binary  # (C, 224, 224) uint8 fluorescence channels
+Metadata_JCP2022, Metadata_InChIKey, Metadata_PlateType                    # source metadata
+perturbation, batch, treatment, Metadata_Perturbation                      # benchmark axes
+```
+
+## Selection recipe
+
+1. All control wells, capped to a small budget.
+2. Treated wells whose perturbation appears in **both** the held-out
+   batch and at least one non-held-out batch (so cross-batch retrieval
+   is reproducible). Per chosen perturbation: one held-out well + one
+   non-held-out well.
+3. Per-well cell cap to keep total budget near 1,000 cells.
+
+Seed = 42. See `build_info.json` for exact stats.
+
+## Quick start
+
+```python
+from datasets import load_dataset
+
+ds = load_dataset("cp-bg-bench-anon/jump-sample", name="crops", split="train")
+print(ds)
+print(ds[0]["row_key"], ds[0]["perturbation"])
+```
+
+## Full dataset
+
+The corresponding full-size release is hosted separately.
+
+## License
+
+JUMP-CP: CC-BY 4.0. RxRx1 / RxRx3-core: CC BY-NC-SA 4.0.
+Verify upstream license terms before use.

aggregated/01_JUMP_DINO_ECFP4_C_aggregated.h5ad

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build_info.json

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+{
+  "dataset": "jump",
+  "held_out_batch_axis_value": "source_4",
+  "target_cells": 1000,
+  "max_cells_per_well": 25,
+  "n_target_wells": 70,
+  "seed": 42,
+  "n_wells": 69,
+  "n_cells_per_variant": {
+    "crops": 913,
+    "crops_density": 913,
+    "seg": 913,
+    "seg_density": 913
+  },
+  "n_perturbations_in_preview": 33,
+  "n_perturbations_in_held_out": 32,
+  "selection": {
+    "n_target_wells": 70,
+    "n_paired_perts_available": 296,
+    "n_paired_perts_chosen": 32,
+    "n_control_wells_chosen": 5,
+    "n_wells_total": 69
+  },
+  "source_aggregated_h5ad": "<full-data>/results/embeddings/01_JUMP_DINO_ECFP4_C_aggregated.h5ad",
+  "source_cp_well_h5ad": "<full-data>/cp_measure/jump_cp_well.h5ad"
+}

cp_measure/jump_cp_well.h5ad

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crops/dataset_info.json

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+  "license": ""
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metadata/quality_filter_report.yml

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