feat(ipred): composable feature modules, classifier pipeline, and layered overlays

.dockerignore

@@ -0,0 +1,36 @@
+# Build artifacts & deps (rebuilt inside the image)
+**/node_modules
+**/dist
+**/.vite
+frontend/dist
+backend/static
+
+# Python envs / caches
+.venv
+.conda-py312
+**/__pycache__
+**/*.pyc
+.pytest_cache
+htmlcov
+.coverage
+
+# Tiled server config, data & catalog (external in production — never bundled)
+.tiled
+tiled/
+
+# Local data, backups, runtime files
+data
+.drafts
+.reset-backups
+*.pid
+.run
+
+# VCS / editor / OS
+.git
+.gitignore
+.idea
+.vscode
+.DS_Store
+
+# Plans / docs not needed in the image
+*.md

.gitignore

@@ -14,11 +14,15 @@ build/
 .env
 
 # Tiled catalog database (binary, regenerated on first run via start_all.sh)
-# The zarr data under .tiled/data/ IS committed so clones get demo data.
 .tiled/catalog.db
 .tiled/catalog.db-shm
 .tiled/catalog.db-wal
 
+# Tiled data written at runtime (drag-and-drop ingest, etc.).
+# Demo datasets already committed under .tiled/data/ stay tracked; new arrays
+# ingested locally are ignored. To commit a new demo dataset, use `git add -f`.
+.tiled/data/
+
 # Runtime Tiled thumbnail containers created on save
 **/*__v_thumbs/
 
@@ -45,3 +49,14 @@ Thumbs.db
 htmlcov/
 .coverage
 coverage.xml
+
+# Vendored SlimSAM weights (~75 MB) — fetch with:
+#   node frontend/scripts/fetch-sam-model.mjs
+frontend/public/models/
+
+# Mark25 / TomoJEPA weights (~365 MB) — keep local; path via TOMOJEPA_WEIGHTS
+ipred/models/*.pth
+ipred/models/*.onnx
+
+# Local runtime caches (feature banks, ipred catalog, etc.)
+.local_data/

.reset-backups/20260630_132922/drafts/0ba9bd25134dd13b.json

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+{"source_key": "tiled:http://127.0.0.1:8010:20260221_135217_petiole22_00006", "saved_at": "2026-06-25T18:59:49.077371+00:00", "payload": {"classes": [{"classId": 1, "label": "sample", "color": "#1f77b4", "isVisible": true}], "slices": {"0": [{"id": "f696603e-d357-4b7e-827e-50ae0b8f5b59", "classId": 1, "kind": "brush", "strokes": [{"points": [955.0629085231768, 1242.1078972346318, 953.2575451316743, 1240.3025318059142, 942.4253647826591, 1233.081070091044, 938.8146379996543, 1229.4703392336091, 917.1502773016241, 1204.1952232315637, 906.318096952609, 1187.9469343731062, 891.875189820589, 1169.8932800859309, 886.4590996460814, 1160.8664529423434, 850.3518318160311, 1086.846470364925, 841.3250148585187, 1054.3498926480095, 830.4928345095035, 1001.9942952152012, 825.0767443349961, 949.6386977823933, 823.2713809434936, 911.7260237793251, 825.0767443349961, 872.0079843475397, 826.8821077264986, 861.1757917752345, 830.4928345095035, 844.9275029167768, 848.5464684245286, 801.5987326275563, 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.reset-backups/20260630_132922/drafts/0ffceac8ef656d85.json

@@ -0,0 +1 @@
+{"source_key": "tiled:http://127.0.0.1:8010:20260221_135217_petiole22_00342", "saved_at": "2026-06-30T18:52:54.249209+00:00", "payload": {"classes": [{"classId": 1, "label": "air", "color": "#1f77b4", "isVisible": true}, {"classId": 2, "label": "xylem", "color": "#ff7f0e", "isVisible": true}], "slices": {}, "split_by_slice": {}, "negative_slices": []}}

.reset-backups/20260630_132922/drafts/1729d6dc86766d96.json

@@ -0,0 +1 @@
+{"source_key": "tiled:http://127.0.0.1:8010:20260221_135217_petiole22_00022", "saved_at": "2026-06-24T22:44:46.981750+00:00", "payload": {"classes": [{"classId": 1, "label": "air", "color": "#1f77b4", "isVisible": true}], "slices": {"0": [{"id": "f148d064-7c7b-4144-a0b2-b077d32a7b72", "classId": 1, "kind": "rectangle", "x": 85.54367013626036, "y": 109.76751444407026, "w": 317.86193476823615, "h": 330.6914795533273}]}, "split_by_slice": {}, "negative_slices": []}}

.reset-backups/20260630_132922/drafts/3492dd4eaa5033bc.json

@@ -0,0 +1 @@
+{"source_key": "tiled:http://127.0.0.1:8010:browse/dataset/octopus_synaps", "saved_at": "2026-06-25T18:13:45.144856+00:00", "payload": {"classes": [], "slices": {}, "split_by_slice": {}, "negative_slices": []}}

.reset-backups/20260630_132922/drafts/3b1855dc641653aa.json

@@ -0,0 +1 @@
+{"source_key": "tiled:http://127.0.0.1:8010:browse/dataset/dino_synaps", "saved_at": "2026-06-25T18:05:44.096931+00:00", "payload": {"classes": [], "slices": {}, "split_by_slice": {}, "negative_slices": []}}

.reset-backups/20260630_132922/drafts/409afa0c1f17a37f.json

@@ -0,0 +1 @@
+{"source_key": "tiled:http://127.0.0.1:8010:20260221_135217_petiole22_00301", "saved_at": "2026-06-30T17:47:08.437224+00:00", "payload": {"classes": [{"classId": 1, "label": "air", "color": "#1f77b4", "isVisible": true}, {"classId": 2, "label": "xylem", "color": "#ff7f0e", "isVisible": true}, {"classId": 3, "label": "phloem", "color": "#2ca02c", "isVisible": true}, {"classId": 4, "label": "void", "color": "#d62728", "isVisible": true}, {"classId": 5, "label": "pith", "color": "#9467bd", "isVisible": true}, {"classId": 6, "label": "cortex", "color": "#8c564b", "isVisible": true}], "slices": {"0": []}, "split_by_slice": {}, "negative_slices": []}}

.reset-backups/20260630_132922/drafts/528391810fd3da0e.json

@@ -0,0 +1 @@
+{"source_key": "tiled:http://127.0.0.1:8010:20260221_135217_petiole22_00000", "saved_at": "2026-06-18T19:00:16.402403+00:00", "payload": {"classes": [{"classId": 2, "label": "plant", "color": "#0fff37", "isVisible": true}], "slices": {}, "split_by_slice": {}, "negative_slices": []}}