bundles/README: trim methodology, keep schema only

bundles/README.md

@@ -1,26 +1,21 @@
 # `bundles/` — per-neuron review JSONs
 
-One JSON per MICrONS neuron, generated from the supervised Stage2 SE3
-model's per-patch inference output.
+One JSON per MICrONS neuron.  Demo data for the **MERGER FREE**
+project by Fuming Yang and Sven Dorkenwald.
 
-## Filename convention
+## Filename
 
 ```
-<latest_root_id>_<partition_method>.json
+<latest_root_id>_<tag>.json.gz
 ```
 
-- `<latest_root_id>` — the current (post-proofread) CAVE root id of
-  the neuron, e.g. `864691134949350652`.
-- `<partition_method>` — how token clusters inside each suspect
-  window were cut.  Currently:
-    - `hybrid` — wsbm if DL ≤ 100, else spectral+
-    - (planned) `spectral` — k-aware spectral cut, no MDL gate
-    - (planned) `wsbm` — Bayesian SBM only
+- `<latest_root_id>` — the current CAVE root id of the neuron.
+- `<tag>` — a short label for the bundle variant (e.g. `hybrid`).
 
 ## Direct download URL
 
 ```
-https://huggingface.co/datasets/FumingY/MergeFree/resolve/main/bundles/<ROOT_ID>_hybrid.json.gz
+https://huggingface.co/datasets/FumingY/MergeFree/resolve/main/bundles/<ROOT_ID>_<TAG>.json.gz
 ```
 
 ## JSON schema (v1)
@@ -31,60 +26,36 @@ https://huggingface.co/datasets/FumingY/MergeFree/resolve/main/bundles/<ROOT_ID>
   "neuron": {
     "latest_root_id":  "864691134949350652",
     "old_root_ids":    ["864691...", "..."],
-    "old_root_id":     "864691...",            // legacy: first old root
+    "old_root_id":     "864691...",
     "datastack":       "minnie65_public"
   },
   "metadata": {
-    "generated_at":     "2026-05-07T12:34:56Z",
-    "n_windows":        1166,
-    "n_suspects":       12,
-    "verify_thresh":    0.05,
-    "partition_method": "hybrid"
+    "generated_at":  "2026-05-07T12:34:56Z",
+    "n_windows":     1166,
+    "n_suspects":    12,
+    "verify_thresh": 0.05
   },
   "windows": [
     {
-      "idx":          0,
-      "center_um":    [123.4, 567.8, 90.1],
-      "verify_prob":  0.07,
-      "is_suspect":   false
+      "idx":         0,
+      "center_um":   [123.4, 567.8, 90.1],
+      "verify_prob": 0.07,
+      "is_suspect":  false
     },
     {
-      "idx":          42,
-      "center_um":    [...],
-      "verify_prob":  0.83,
-      "is_suspect":   true,
+      "idx":         42,
+      "center_um":   [...],
+      "verify_prob": 0.83,
+      "is_suspect":  true,
       "tokens": {
-        "pos_rel_um": [[x, y, z], ...],   // token positions relative to center_um
-        "labels":     [0, 0, 1, 1, 2, ...], // cluster id per token
-        "spectral":   {
-          "k":               2,
-          "score":           0.71,         // spectral+ score (when method=spectral_plus / hybrid→spectral+)
-          "hybrid_decision": "spectral+",  // present when method=hybrid: which backend was used
-          "wsbm_dl":         412.18        // wsbm best DL (always present in hybrid bundles)
-        }
+        "pos_rel_um": [[x, y, z], ...],
+        "labels":     [0, 0, 1, 1, 2, ...]
       }
     }
   ]
 }
 ```
 
-## Pipeline (offline)
-
-1. **Suspect filter**: `verify_prob ≥ 0.05`
-2. **Spectral+ heuristic**: demote tied per-k scores or mean < 0.5
-3. **Spatial NMS**: radius 9 µm
-4. **wSBM uniform-DL filter**: demote when per-k DL is uniform
-   (max−min ≤ 0.01) AND max ≤ 250 — strong "no block structure"
-   signal
-5. **Cut method (hybrid)**: per surviving suspect, run wsbm.  If its
-   chosen-k DL ≤ 100 use wsbm's labels (incl. k=1 = no cut); else
-   fall back to spectral+ for boundary recall.
-
-`old_root_ids` come from `mesh.npz` → `mesh_coverage_cache.npz` →
-`manifest.json` (the same lookup `export_review_bundle.py` does).
-The static review site uses them to overlay pre-proofread segments
-in red on top of the current segmentation.
-
 ## Reviewer workflow
 
 See the top-level [README](../README.md).