3d-brain-animations

name

3d-brain-animations

description

Render 3D still images and rotating turntable animations of brain regions from ANY BrainGlobe atlas (mouse, rat, human, zebrafish, etc.), with optional glow/bloom highlighting and a semi-transparent whole-brain shell for context. Use this WHENEVER the user wants to visualize, render, picture, or animate brain anatomy: any species, any region (hippocampus, CA1, dentate gyrus, cortex, thalamus, amygdala, ...), any color, a glowing/highlighted region, a rotating brain video, or a neuroanatomy figure for a paper/thesis/slide — even if they don't mention Blender or BrainGlobe. Handles requests like "rotating animation of the rat hippocampus CA1 glowing purple while the rest of the brain is semi-transparent". The skill installs anything missing and renders via bundled scripts, so do NOT write Blender/bpy code or probe the API.

3D Brain Animations

Turns a natural-language request into a 3D brain figure or animation. All logic is in bundled scripts; a render is two bash calls plus a small JSON spec. Never write bpy/Blender code or introspect the API — translate the request into a spec and call the scripts. (macOS; Blender installed. First use installs deps + the add-on and downloads the atlas, a few minutes; later runs are instant.)

scripts/run.sh auto-locates the installed Blender. Use absolute paths to this skill.

Translate the request, then run two commands

From the user's words, fill in a spec:

• Species → atlas (pass to setup and put in the spec as atlas):

  says	atlas
  mouse	allen_mouse_25um (small/fast test: allen_mouse_100um)
  rat	whs_sd_rat_39um
  human	allen_human_500um
  zebrafish	mpin_zfish_1um
  other / unsure	run bash scripts/run.sh find <guess_atlas> <kw>, or ask

  If the user names a species without an atlas, use the standard one above and say which you chose.

• Region(s) are given by atlas-specific acronym. If the user uses plain words ("hippocampus", "dentate gyrus") or you're unsure of the acronym for this atlas, resolve it first: bash scripts/run.sh find <atlas> <keyword> → prints acronym <tab> name. (E.g. CA1 is CA1 in Allen mouse but the rat atlas also has DG, SUB, etc.) After rendering, confirm each region appears in RESULT's loaded list; if one was skipped, the acronym was wrong — find it.

• "rest of the brain semi-transparent" / "whole brain" / "in context" → "envelope": "auto" (resolves the whole-brain shell for any atlas automatically). Omit envelope for no shell.

• Color words → RGB (0–1): purple [0.5,0.05,1], blue [0.05,0.25,1], green [0.18,0.82,0.4], red [0.93,0.2,0.24], orange [0.99,0.52,0.13], yellow [1,0.85,0.1], cyan/teal [0.1,0.74,0.84], pink [0.99,0.38,0.72]. "glowing"/"highlight"/"lit up" → "glow": true.

• "rotating"/"animation"/"video"/"turntable" → "mode": "anim". "full rotation" → one rotation (rotations_per_phase: 1). Multiple regions appearing one-by-one → reveal: "sequential_solo" (each alone) or "sequential_cumulative" (each adds on). Everything lit the whole time → "all".

Then:

bash scripts/run.sh setup <atlas>          # idempotent; ends in READY
bash scripts/run.sh render /tmp/spec.json  # prints RESULT {...output...}

Stills → <output>.png; animations → <output>.mp4 (frames also in /tmp/bb_frames/). Animations render many frames (minutes) — run the render command in the background. To show the result: Read the .png; for an .mp4, Read a couple of /tmp/bb_frames/f_*.png to verify and give the user the .mp4 path.

Spec schema

Required: atlas, regions, output. Everything else defaults sensibly (dark background, auto-framed camera, 3-light setup, EEVEE). Colors are [r,g,b] 0–1.

{
  "mode": "still",                 // "still" (default) | "anim"
  "atlas": "whs_sd_rat_39um",
  "output": "/Users/<you>/Desktop/figure",   // .png/.mp4 appended automatically
  "envelope": "auto",              // "auto" = whole-brain shell | a specific acronym | omit for none
  "envelope_alpha": 0.10,          // lower = more transparent
  "regions": [
    {"acronym": "CA1", "color": [0.5,0.05,1.0], "glow": true}   // color/glow/alpha optional
  ],
  "glow": {"emission":1.3,"strength":0.8,"size":0.32,"threshold":0.7,"saturation":1.2}, // optional
  "resolution": [1600,1100],       // anim default 1280x720
  "samples": 32,
  "view_dir": [0.5,-1.0,0.32],
  "background": [0.02,0.022,0.03],
  "anim": {                        // only when mode=="anim"
    "fps": 30, "deg_per_frame": 1.5,         // smaller = slower spin
    "reveal": "sequential_solo",             // sequential_solo | sequential_cumulative | all
    "rotations_per_phase": 1, "final_together_rotations": 1, "fade_frames": 20
  }
}

Examples (request → spec)

"Rotating animation, full rotation of the rat hippocampus CA1 glowing purple, rest of the brain semi-transparent" (find whs_sd_rat_39um CA1 confirms acronym CA1):

{"mode":"anim","atlas":"whs_sd_rat_39um","output":"/Users/me/Desktop/ca1_spin",
 "envelope":"auto",
 "regions":[{"acronym":"CA1","color":[0.5,0.05,1.0],"glow":true}],
 "anim":{"reveal":"all","rotations_per_phase":1,"deg_per_frame":1.5}}

Same request for human → just "atlas":"allen_human_500um" (and setup allen_human_500um); for mouse → "atlas":"allen_mouse_25um". The acronym may differ per atlas, so find it.

Two regions revealed one at a time, then together (animation):

{"mode":"anim","atlas":"whs_sd_rat_39um","output":"/Users/me/Desktop/hippo",
 "envelope":"auto",
 "regions":[{"acronym":"CA1","color":[0.05,0.25,1.0],"glow":true},
            {"acronym":"DG","color":[0.50,0.05,1.0],"glow":true}],
 "anim":{"reveal":"sequential_solo","rotations_per_phase":1,"final_together_rotations":1}}

Still figure, several solid-colored regions in a glass brain:

{"atlas":"allen_mouse_25um","output":"/Users/me/Desktop/mouse_fig","envelope":"auto",
 "regions":[{"acronym":"HPF","color":[0.16,0.42,0.98]},{"acronym":"TH","color":[0.99,0.52,0.13]}]}

Notes

• Glow more: raise glow.emission (~1.3→1.6) and glow.strength (~0.8→1.0); keep emission under ~1.8 or colors wash to white.
• setup printing NOT_READY: read its STATUS — the atlas may be mid-download or the add-on install needs network.
• A region missing from RESULT.loaded means a wrong/mesh-less acronym; use find to fix it.
• The Blender MCP "connector" (live GUI) is optional; this skill runs Blender headless, which is reliable and cheap. If a live MCP Blender is connected you may open the produced .blend/frames there instead, but headless is the default.