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Deploy full MindVisualizer Python runtime

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  1. .dockerignore +8 -0
  2. .gitattributes +1 -0
  3. .gitignore +5 -0
  4. Dockerfile +43 -0
  5. README.md +7 -5
  6. data/brain_alignment.json +28 -0
  7. data/extra_parcellation/README.md +53 -0
  8. data/extra_parcellation/combined_atlas.nii.gz +3 -0
  9. data/extra_parcellation/combined_atlas_labels.json +129 -0
  10. data/label_grid_cache.keys.json +1 -0
  11. data/label_grid_cache.npz +3 -0
  12. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_entropy.bin +3 -0
  13. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_mean_xyz3.bin +3 -0
  14. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_meta.json +1 -0
  15. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_mu1_xyz3.bin +3 -0
  16. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_mu2_xyz3.bin +3 -0
  17. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_mu3_xyz3.bin +3 -0
  18. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_mu4_xyz3.bin +3 -0
  19. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_mu5_xyz3.bin +3 -0
  20. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_mu6_xyz3.bin +3 -0
  21. data/mdn/mdn_particles_rdcim_teacher_edge_hq_grid125_pi_xyz6.bin +3 -0
  22. data/mdn/mdn_particles_rdcim_teacher_edge_hq_training_points.npy +3 -0
  23. data/meshes/.keep +1 -0
  24. data/meshes_obj/10153.obj +3 -0
  25. data/meshes_obj/10154.obj +3 -0
  26. data/meshes_obj/10155.obj +3 -0
  27. data/meshes_obj/10156.obj +3 -0
  28. data/meshes_obj/10157.obj +3 -0
  29. data/meshes_obj/10158.obj +3 -0
  30. data/meshes_obj/10159.obj +3 -0
  31. data/meshes_obj/10292.obj +3 -0
  32. data/meshes_obj/10306.obj +3 -0
  33. data/meshes_obj/10307.obj +3 -0
  34. data/meshes_obj/10308.obj +3 -0
  35. data/meshes_obj/10311.obj +3 -0
  36. data/meshes_obj/10313.obj +3 -0
  37. data/meshes_obj/10327.obj +3 -0
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  40. data/meshes_obj/10331.obj +3 -0
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  46. data/meshes_obj/10337.obj +3 -0
  47. data/meshes_obj/10338.obj +3 -0
  48. data/meshes_obj/10339.obj +3 -0
  49. data/meshes_obj/10342.obj +3 -0
  50. data/meshes_obj/10343.obj +3 -0
.dockerignore ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
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+ .git
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+ .idea
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+ .venv
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+ __pycache__
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+ *.pyc
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+ *.pyo
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+ .env
8
+ data/meshes
.gitattributes CHANGED
@@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
33
  *.zip filter=lfs diff=lfs merge=lfs -text
34
  *.zst filter=lfs diff=lfs merge=lfs -text
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  *tfevents* filter=lfs diff=lfs merge=lfs -text
 
 
33
  *.zip filter=lfs diff=lfs merge=lfs -text
34
  *.zst filter=lfs diff=lfs merge=lfs -text
35
  *tfevents* filter=lfs diff=lfs merge=lfs -text
36
+ *.obj filter=lfs diff=lfs merge=lfs -text
.gitignore ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
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+ .cache/
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+ __pycache__/
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+ *.pyc
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+ *.pyo
5
+ .env
Dockerfile ADDED
@@ -0,0 +1,43 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ FROM python:3.11-slim
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+
3
+ ENV DEBIAN_FRONTEND=noninteractive \
4
+ DISPLAY=:99 \
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+ LIBGL_ALWAYS_SOFTWARE=1 \
6
+ MESA_GL_VERSION_OVERRIDE=3.3 \
7
+ PIP_NO_CACHE_DIR=1 \
8
+ PYTHONUNBUFFERED=1
9
+
10
+ RUN apt-get update && apt-get install -y --no-install-recommends \
11
+ ca-certificates \
12
+ fluxbox \
13
+ libegl1 \
14
+ libgl1 \
15
+ libgl1-mesa-dri \
16
+ libglib2.0-0 \
17
+ libglu1-mesa \
18
+ libsm6 \
19
+ libx11-6 \
20
+ libxext6 \
21
+ libxrender1 \
22
+ libxt6 \
23
+ novnc \
24
+ websockify \
25
+ x11vnc \
26
+ xterm \
27
+ xvfb \
28
+ && rm -rf /var/lib/apt/lists/*
29
+
30
+ WORKDIR /app/mindVisualizer
31
+ COPY . /app/mindVisualizer
32
+
33
+ RUN python -m pip install --upgrade pip setuptools wheel && \
34
+ python -m pip install \
35
+ numpy scipy vtk \
36
+ langchain langchain-openai langchain-community \
37
+ faiss-cpu python-dotenv certifi tiktoken openai \
38
+ brainglobe-atlasapi nibabel nilearn scikit-image && \
39
+ chmod +x /app/mindVisualizer/start.sh
40
+
41
+ EXPOSE 7860
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+
43
+ CMD ["/app/mindVisualizer/start.sh"]
README.md CHANGED
@@ -1,10 +1,12 @@
1
- ---
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- title: Mindvisualizer Live
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- emoji: 💻
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- colorFrom: indigo
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  colorTo: blue
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  sdk: docker
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  pinned: false
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  ---
9
 
10
- Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
 
 
 
1
+ ---
2
+ title: MindVisualizer Live
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+ emoji: 🧠
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+ colorFrom: green
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  colorTo: blue
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  sdk: docker
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  pinned: false
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  ---
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+ # MindVisualizer Live
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+
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+ Runs the full Python/VTK MindVisualizer desktop runtime through noVNC.
data/brain_alignment.json ADDED
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data/extra_parcellation/README.md ADDED
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+ # Extra Parcellation Data
2
+
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+ Provides fine-grained subregion labels alongside the primary Allen atlas meshes.
4
+
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+ ## Setup (recommended)
6
+
7
+ Run the setup script to build the combined atlas automatically:
8
+
9
+ ```bash
10
+ python scripts/setup_extra_parcellation.py
11
+ ```
12
+
13
+ This downloads and merges three complementary MNI-space atlases via nilearn:
14
+
15
+ | Layer | Source | Regions | Role |
16
+ |-------|--------|---------|------|
17
+ | 1 | Harvard-Oxford Cortical | 48 | Broad cortical coverage |
18
+ | 2 | Harvard-Oxford Subcortical | 17 | Thalamus, putamen, caudate, hippocampus, amygdala, etc. |
19
+ | 3 | **Julich-Brain** (highest priority) | 62 | Cytoarchitectonic: motor BA4a/4p, somatosensory BA1-3, visual V1-V5, auditory, Broca's, hippocampal subfields |
20
+
21
+ **Total: 127 labeled regions**, Julich-Brain labels override coarser Harvard-Oxford
22
+ where available.
23
+
24
+ Output files (auto-detected by flow mode):
25
+ - `combined_atlas.nii.gz` — NIfTI volume (~700KB)
26
+ - `combined_atlas_labels.json` — label ID to name map
27
+
28
+ ## How it works
29
+
30
+ The combined atlas is in MNI152 1mm space. The Allen atlas scene space is
31
+ approximately MNI-aligned, so probe coordinates can be used directly for lookups.
32
+ When the exact voxel is unlabeled, a nearby-search fallback finds the closest
33
+ labeled region within a few mm.
34
+
35
+ When both the primary Allen mesh and the extra parcellation cover a probe position,
36
+ both are highlighted: the Allen mesh in red, the extra parcellation subregion in
37
+ orange. The subregion name is included in the LLM context as additional detail.
38
+
39
+ ## Custom atlas
40
+
41
+ You can also provide any NIfTI atlas in MNI space:
42
+
43
+ ```bash
44
+ python examples/flow_probe_example.py \
45
+ --extra-parcellation my_atlas.nii.gz \
46
+ --extra-parcellation-labels my_atlas_labels.json
47
+ ```
48
+
49
+ ## Requirements
50
+
51
+ ```bash
52
+ pip install nilearn nibabel scikit-image
53
+ ```
data/extra_parcellation/combined_atlas.nii.gz ADDED
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data/extra_parcellation/combined_atlas_labels.json ADDED
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1
+ {
2
+ "1": "Frontal Pole",
3
+ "2": "Insular Cortex",
4
+ "3": "Superior Frontal Gyrus",
5
+ "4": "Middle Frontal Gyrus",
6
+ "5": "Inferior Frontal Gyrus, pars triangularis",
7
+ "6": "Inferior Frontal Gyrus, pars opercularis",
8
+ "7": "Precentral Gyrus",
9
+ "8": "Temporal Pole",
10
+ "9": "Superior Temporal Gyrus, anterior division",
11
+ "10": "Superior Temporal Gyrus, posterior division",
12
+ "11": "Middle Temporal Gyrus, anterior division",
13
+ "12": "Middle Temporal Gyrus, posterior division",
14
+ "13": "Middle Temporal Gyrus, temporooccipital part",
15
+ "14": "Inferior Temporal Gyrus, anterior division",
16
+ "15": "Inferior Temporal Gyrus, posterior division",
17
+ "16": "Inferior Temporal Gyrus, temporooccipital part",
18
+ "17": "Postcentral Gyrus",
19
+ "18": "Superior Parietal Lobule",
20
+ "19": "Supramarginal Gyrus, anterior division",
21
+ "20": "Supramarginal Gyrus, posterior division",
22
+ "21": "Angular Gyrus",
23
+ "22": "Lateral Occipital Cortex, superior division",
24
+ "23": "Lateral Occipital Cortex, inferior division",
25
+ "24": "Intracalcarine Cortex",
26
+ "25": "Frontal Medial Cortex",
27
+ "26": "Juxtapositional Lobule Cortex (formerly Supplementary Motor Cortex)",
28
+ "27": "Subcallosal Cortex",
29
+ "28": "Paracingulate Gyrus",
30
+ "29": "Cingulate Gyrus, anterior division",
31
+ "30": "Cingulate Gyrus, posterior division",
32
+ "31": "Precuneous Cortex",
33
+ "32": "Cuneal Cortex",
34
+ "33": "Frontal Orbital Cortex",
35
+ "34": "Parahippocampal Gyrus, anterior division",
36
+ "35": "Parahippocampal Gyrus, posterior division",
37
+ "36": "Lingual Gyrus",
38
+ "37": "Temporal Fusiform Cortex, anterior division",
39
+ "38": "Temporal Fusiform Cortex, posterior division",
40
+ "39": "Temporal Occipital Fusiform Cortex",
41
+ "40": "Occipital Fusiform Gyrus",
42
+ "41": "Frontal Opercular Cortex",
43
+ "42": "Central Opercular Cortex",
44
+ "43": "Parietal Opercular Cortex",
45
+ "44": "Planum Polare",
46
+ "45": "Heschl's Gyrus (includes H1 and H2)",
47
+ "46": "Planum Temporale",
48
+ "47": "Supracalcarine Cortex",
49
+ "48": "Occipital Pole",
50
+ "103": "Left Lateral Ventricle",
51
+ "104": "Left Thalamus",
52
+ "105": "Left Caudate",
53
+ "106": "Left Putamen",
54
+ "107": "Left Pallidum",
55
+ "108": "Brain-Stem",
56
+ "109": "Left Hippocampus",
57
+ "110": "Left Amygdala",
58
+ "111": "Left Accumbens",
59
+ "114": "Right Lateral Ventricle",
60
+ "115": "Right Thalamus",
61
+ "116": "Right Caudate",
62
+ "117": "Right Putamen",
63
+ "118": "Right Pallidum",
64
+ "119": "Right Hippocampus",
65
+ "120": "Right Amygdala",
66
+ "121": "Right Accumbens",
67
+ "201": "Amygdala_centromedial group",
68
+ "202": "Amygdala_laterobasal group",
69
+ "203": "Amygdala_superficial group",
70
+ "204": "Anterior intra-parietal sulcus hIP1",
71
+ "205": "Anterior intra-parietal sulcus hIP2",
72
+ "206": "Anterior intra-parietal sulcus hIP3",
73
+ "207": "Broca's area BA44",
74
+ "208": "Broca's area BA45",
75
+ "209": "Hippocampus cornu ammonis",
76
+ "210": "Hippocampus dentate gyrus",
77
+ "211": "Hippocampus entorhinal cortex",
78
+ "212": "Hippocampus hippocampal-amygdaloid transition area",
79
+ "213": "Hippocampus subiculum",
80
+ "214": "Inferior parietal lobule PF",
81
+ "215": "Inferior parietal lobule PFcm",
82
+ "216": "Inferior parietal lobule PFm",
83
+ "217": "Inferior parietal lobule PFop",
84
+ "218": "Inferior parietal lobule PFt",
85
+ "219": "Inferior parietal lobule PGp",
86
+ "220": "Inferior parietal lobule Pga",
87
+ "221": "Insula Id1",
88
+ "222": "Insula Ig1",
89
+ "223": "Insula Ig2",
90
+ "224": "Lateral geniculate body",
91
+ "225": "Mamillary body",
92
+ "226": "Medial geniculate body",
93
+ "227": "Premotor cortex BA6",
94
+ "228": "Primary auditory cortex TE1.0",
95
+ "229": "Primary auditory cortex TE1.1",
96
+ "230": "Primary auditory cortex TE1.2",
97
+ "231": "Primary motor cortex BA4a",
98
+ "232": "Primary motor cortex BA4p",
99
+ "233": "Primary somatosensory cortex BA1",
100
+ "234": "Primary somatosensory cortex BA2",
101
+ "235": "Primary somatosensory cortex BA3a",
102
+ "236": "Primary somatosensory cortex BA3b",
103
+ "237": "Secondary somatosensory cortex / Parietal operculum OP1",
104
+ "238": "Secondary somatosensory cortex / Parietal operculum OP2",
105
+ "239": "Secondary somatosensory cortex / Parietal operculum OP3",
106
+ "240": "Secondary somatosensory cortex / Parietal operculum OP4",
107
+ "241": "Superior parietal lobule 5Ci",
108
+ "242": "Superior parietal lobule 5L",
109
+ "243": "Superior parietal lobule 5M",
110
+ "244": "Superior parietal lobule 7A",
111
+ "245": "Superior parietal lobule 7M",
112
+ "246": "Superior parietal lobule 7P",
113
+ "247": "Superior parietal lobule 7PC",
114
+ "248": "Visual cortex V1 BA17",
115
+ "249": "Visual cortex V2 BA18",
116
+ "250": "Visual cortex V3V",
117
+ "251": "Visual cortex V4",
118
+ "252": "Visual cortex V5",
119
+ "253": "WM: Acoustic radiation",
120
+ "254": "WM: Callosal body",
121
+ "255": "WM: Cingulum",
122
+ "256": "WM: Corticospinal tract",
123
+ "257": "WM: Fornix",
124
+ "258": "WM: Inferior occipito-frontal fascicle",
125
+ "259": "WM: Optic radiation",
126
+ "260": "WM: Superior longitudinal fascicle",
127
+ "261": "WM: Superior occipito-frontal fascicle",
128
+ "262": "WM: Uncinate fascicle"
129
+ }
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