Virtual staining

virtual-staining/README.md

@@ -0,0 +1,51 @@
+# Virtual staining evaluation
+
+Reproduce paper metrics for five models on IMC virtual-staining task.
+
+## Quick start (paper reproduction)
+
+```bash
+python3 evaluate_all.py --config configs/paper.yaml --table
+python3 evaluate_all.py plot --results results/per_point_results.csv
+```
+
+## Input data format
+
+### `immuvis_npz` — used by ImmuVis models
+
+Each file is named `recn-{image_id}.npz` and contains:
+
+| Key | Shape | Content |
+|---|---|---|
+| `recon` | `(C, H, W)` | Model predictions, one channel per marker |
+| `target` | `(C, H, W)` | Ground truth, same channel ordering |
+| `marker_names` | `(C,)` | Array of marker name strings |
+| `metadata` | scalar (JSON string) | `{"image_path": "...", "dataset_name": "hn"}` |
+
+Image ID is extracted from `metadata["image_path"]` by taking the filename stem (last `/`-separated component, minus extension).
+
+Predictions/ground truth are indexed by `[channel, :, :]` — the `marker_names` array is searched for the target marker name to find the channel index.
+
+### `virtues_npy` — used by Virtues and Eva models
+
+Directory of single-channel `.npy` files named `{image_id}_{marker}_recon.npy`, each shape `(H, W)`.
+
+Marker names in filenames use underscores and short forms; they are normalised on load:
+
+| Filename marker | Canonical name |
+|---|---|
+| `Carbonic` | `Carbonic Anhydrase` |
+| `PARP` | `cl.PARP` |
+| `H3` or `Histone` | `Histone H3` |
+| `Carbonic_Anhydrase` | `Carbonic Anhydrase` (underscores → spaces) |
+
+No ground truth is stored in these files. Ground truth is always sourced from a separate `immuvis_npz` model (configured via `ground_truth.source_model`).
+
+## Output
+
+All CSVs in `output_dir/` (default `results/`):
+
+- `per_point_results.csv` — per (model, image, marker) MSE + Pearson
+- `per_marker_pearson.csv` — per-marker aggregated Pearson (sufficient statistics)
+- `summary.csv` — per-(model, marker) mean ± std
+- `boxplot.pdf` — grouped box plot via `plot` subcommand

virtual-staining/configs/paper.yaml

@@ -0,0 +1,58 @@
+marker_stats_csv: "data/marker_ds_stats.csv"
+crop_size: [128, 128]
+output_dir: "results"
+
+models:
+
+  - name: "virtues_our_norm"
+    path: "/raid_encrypted/immucan/recons/virtues_our_norm/"
+    format: "virtues_npy"
+    display_name: "Virtues_{IMC17M}_{OP}"
+    prediction_transform:
+      type: "immu_offset"
+      params: { scale: 3.4 }
+    ground_truth:
+      source_model: "immuvis_612"
+      transform:
+        type: "immu_offset"
+        params: { scale: 3.4 }
+
+  - name: "eva_hn_recon_crop"
+    path: "/raid_encrypted/immucan/recons/eva_hn_recon_crop/"
+    format: "virtues_npy"
+    display_name: "EVA_{OP}"
+    prediction_transform:
+      type: "immu_offset"
+      params: { scale: 3.4 }
+    ground_truth:
+      source_model: "immuvis_612"
+      transform:
+        type: "immu_offset"
+        params: { scale: 3.4 }
+
+  - name: "immuvis_609"
+    path: "/raid_encrypted/immucan/results/with_reconstructs/recons/immuvis_609_loo/"
+    format: "immuvis_npz"
+    display_name: "ImmuVis_{ViT}"
+    filter_pairs_to: "virtues_our_norm"
+    prediction_transform:
+      type: "immu_offset"
+      params: { scale: 3.4 }
+
+  - name: "immuvis_612"
+    path: "/raid_encrypted/immucan/results/with_reconstructs/recons/immuvis_612_loo/"
+    format: "immuvis_npz"
+    display_name: "ImmuVis_{Conv}"
+    filter_pairs_to: "virtues_our_norm"
+    prediction_transform:
+      type: "immu_offset"
+      params: { scale: 3.4 }
+
+  - name: "immuvis_622"
+    path: "/raid_encrypted/immucan/results/with_reconstructs/recons/immuvis_622_loo/"
+    format: "immuvis_npz"
+    display_name: "ImmuVis_{Swin}"
+    filter_pairs_to: "virtues_our_norm"
+    prediction_transform:
+      type: "immu_offset"
+      params: { scale: 3.4 }

virtual-staining/configs/swin.yaml

@@ -0,0 +1,31 @@
+marker_stats_csv: "data/marker_ds_stats.csv"
+crop_size: [128, 128]
+output_dir: "results_swin"
+
+models:
+  - name: "virtues_our_norm"
+    path: "/raid_encrypted/immucan/recons/virtues_our_norm/"
+    format: "virtues_npy"
+    display_name: "Virtues_{IMC17M}_{OP}"
+    prediction_transform:
+      type: "immu_offset"
+      params: { scale: 3.4 }
+    ground_truth:
+      source_model: "immuvis_612"
+      transform:
+        type: "immu_offset"
+        params: { scale: 3.4 }
+
+  - name: "immuvis_612"
+    path: "/raid_encrypted/immucan/results/with_reconstructs/recons/immuvis_612_loo/"
+    format: "immuvis_npz"
+    evaluate: false
+
+  - name: "immuvis_622"
+    path: "/raid_encrypted/immucan/results/with_reconstructs/recons/immuvis_622_loo/"
+    format: "immuvis_npz"
+    display_name: "ImmuVis_{Swin}"
+    filter_pairs_to: "virtues_our_norm"
+    prediction_transform:
+      type: "immu_offset"
+      params: { scale: 3.4 }