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CineMap logo

CineMap

Cinematic videos from large-scale EM segmentation data.
Scout in Neuroglancer, render in Blender.

Example CineMap render

An example shot rendered with CineMap.

CineMap interface

How it works

CineMap turns Neuroglancer views into a keyframe timeline that Blender renders into a smooth video.

Neuroglancer is not the renderer — it is your control surface. You arrange the scene exactly how you want it in Neuroglancer (and frame it in the 3D preview), then capture it as a keyframe. Blender generates the actual frames.

Quick start

1. Paste your Neuroglancer state link into the field and click Create.

Create a project

2. Scout freely in the Neuroglancer pane — choose layers, segments, colors, whatever you want to show.

3. Capture the view. Click ★ Bake keyframe to save the current view as a new keyframe, or ⟳ Update current frame to overwrite the selected one. Each keyframe becomes one Blender frame.

Framing buttons

What a keyframe captures

Baking (or updating) a keyframe records the full state of your view:

  • Visible layers — which Neuroglancer layers are shown
  • Visible segments — for mesh layers, which segment IDs are on
  • Segment colors — the exact colors from Neuroglancer
  • 3D mesh opacity & silhouette — the mesh rendering style
  • Camera — position, zoom, and rotation, taken from the 3D preview panel

To frame a shot, use the 3D preview (right pane): zoom in, zoom out, and rotate there — that camera is what gets baked.

Working with the timeline

  • Preview the motion — click ▷ Preview to see the interpolated animation between your keyframes.
  • Update a frame — select a keyframe and ⟳ Update current frame to replace it with your latest view.
  • Copy / paste frames — select a keyframe, then use the copy/paste buttons or Ctrl-C / Ctrl-V to duplicate its camera and layer state.
  • Reorder frames — drag keyframes along the timeline to change their order.
  • Add plane sweeps — EM slice sweeps and mesh cutaways live in the lower sweep lane, independent of camera keyframes; disable a sweep to keep it on the timeline but out of preview/export renders.
  • Import / Export project — save and reload a whole project with ⭱ Import / ⭳ Export.

Exporting

  • ⬇ Export video — render the full shot to an mp4.
  • ⬇ Export .blend — a self-contained Blender file (camera, meshes, EM slices, packed textures) for manual finishing.
  • ⟳ Render all fills keyframe thumbnails and sweep preview strips; full exports still render enabled slices and cutaways from the timeline.

Export buttons

Run locally

mamba create -y -n mv_env python=3.11
conda run -n mv_env pip install -e .     # installs all deps incl. bpy (Blender/Cycles)
./run.sh                                 # -> http://0.0.0.0:8000

Requires an NVIDIA GPU (OPTIX / Cycles) and network access to the data host (data is read over https; /nrs need not be mounted).

Choosing a GPU. By default the renderer uses every available NVIDIA GPU. On a multi-GPU machine, set CINEMAP_GPU to pick one (or several) by index — the render log prints OPTIX GPUs available: [0:…, 1:…] so you know the indices:

CINEMAP_GPU=1   ./run.sh      # render only on GPU 1
CINEMAP_GPU=0,2 ./run.sh      # render on GPUs 0 and 2

Let Claude help

Click ✦ Help me! Claude to open the director panel and just ask in plain language — "orbit the nuclei, then sweep a z-slice". Claude builds the keyframes for you.

Help me! Claude

Everything Claude creates is normal keyframes, so you stay in control — tweak, reframe, reorder, or re-bake any of them afterward exactly as if you'd made them by hand. (Requires ANTHROPIC_API_KEY.)