Skip to content

Inspect in 3D

A 3D cube of the tissue volume, with the image and cell labels layered on, swings about 112° and back as the pointer drags the camera.

Place a cube window on the map, then orbit and slice image, labels and transcripts together.

import milume
w = milume.peek(sdata, image="mosaic", labels="cells")  # press I, then click the tissue
w.volume_cut  # cut-plane state after you slide the cross-section

Entering Inspect

Press I or click Inspect, then click the tissue to place a cube window. The top pill shows the window size, Save window and Exit Inspect (Esc).

The Inspect cube open: the top pill shows Exit, Inspect with the window size in µm, Save window, and full screen; the bottom toolbar has camera presets and layer toggles. The Inspect cube open: the top pill shows Exit, Inspect with the window size in µm, Save window, and full screen; the bottom toolbar has camera presets and layer toggles.

Inspect toolbar

The Inspect toolbar under the cube. Amber callouts: 1 camera Top / Iso / Side, 2 Move and Reset view, 3 Image, 4 Labels, 5 Points (Cross-section sits to their right). The Inspect toolbar under the cube. Amber callouts: 1 camera Top / Iso / Side, 2 Move and Reset view, 3 Image, 4 Labels, 5 Points (Cross-section sits to their right).
Control What it does
1 Top / Iso / Side Snap the camera to a top, oblique or side view.
2 Move Drag to pan the cube window on the map.
Reset view Return the cube camera to its default.
3 Image Show or hide the image layer. Right-click for palette, contrast, alpha, gamma and projection.
4 Labels Show or hide the labels layer. Right-click for projection and fill. Cell outlines stay on.
5 Points Show or hide the points layer.
Cross-section Slide a cut plane through the cube.

Cross-section

The pointer drags the cut slider: a cross-section plane sweeps through the cube and back; cell outlines stay visible on the cut.

Python

w.inspect_cx, w.inspect_cy, w.inspect_size_um  # window center and size
w.volume_cut                                  # cut-plane state

See Synced traitlets for the volume fields, and pass image= / labels= to milume.peek in Constructor parameters.

Navigate →Pan, zoom, minimap Color & layers →What colors the cells Probe →Raster similarity