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3D viewer guide

How to explore the 3D connectome datasets — especially the large ones (tens of thousands of neurons). The viewer streams each dataset as a level-of-detail (LOD) tile pyramid, so you never have to load every neuron at full resolution at once.

How the level-of-detail pyramid works

Each dataset is cut into an octree of 3D-Tiles. The key idea:

• Zoom 0 (zoomed all the way out) is a single coarse tile containing the entire dataset — every neuron, at low resolution. This is where you see the whole thing at once.
• Zooming in loads progressively finer, higher-detail tiles, but only for the region in view. The viewer (LOD = Dynamic) automatically picks the right level for your camera.

So the way to read a big dataset is top-down: look at the whole shape first, then dive into a region.

Recommended workflow for very large datasets

1. Start zoomed out. The full dataset is already visible as the coarse zoom-0 tile — get oriented with the overall morphology before doing anything else.
2. Turn on the Overview panel (right sidebar → Overview → Enable overview). It keeps a small map of the whole dataset visible while you zoom into detail, so you don't lose context.
3. Zoom into a region to inspect detail — only that region's fine tiles load, keeping things fast.
4. If it ever feels heavy, switch Level of Detail to Force Zoom and pick a low zoom level — this caps how much detail is loaded (great for a smooth overview of everything), or lower the Budget (GPU memory) slider at the bottom.

Finding and coloring neurons

• Color By — recolor every neuron by an annotation: cell type, class, super class, predicted neurotransmitter, side, region, dimorphism, etc. (The default, Original, gives each neuron its own colour.) This is the fastest way to make structure pop — e.g. colour a whole-CNS dataset by Super Class to separate descending from ascending neurons.
• Filter by — show only the neurons matching a value (e.g. only one cell type).
• Search features — jump to a neuron by name; the checklist on the left toggles individual neurons on and off.
• Click a neuron in the 3D view to open its info panel with all its annotations.

Other controls

• Slice Plane — clip the dataset along X/Y/Z to see inside dense regions.
• Background — Dark / Light / White.
• Screenshot (S) — save the current view.

In short: zoom out to see everything, enable Overview, then zoom in where it matters — and use Force Zoom or the Budget slider if a very large dataset gets sluggish.