| 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>
bash scripts/run.sh render /tmp/spec.json
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",
"atlas": "whs_sd_rat_39um",
"output": "/Users/<you>/Desktop/figure",
"envelope": "auto",
"envelope_alpha": 0.10,
"regions": [
{"acronym": "CA1", "color": [0.5,0.05,1.0], "glow": true}
],
"glow": {"emission":1.3,"strength":0.8,"size":0.32,"threshold":0.7,"saturation":1.2},
"resolution": [1600,1100],
"samples": 32,
"view_dir": [0.5,-1.0,0.32],
"background": [0.02,0.022,0.03],
"anim": {
"fps": 30, "deg_per_frame": 1.5,
"reveal": "sequential_solo",
"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.
