02 Scientific software · 3D morphology

Organoid Explorer

Which cells have similar 3D shapes? This macOS app, published as Organoid Atlas, links quantitative shape comparisons to reconstructed surfaces and the original microscopy.

Swift
Cellpose-SAM
u-Segment3D
3D morphometry

Watch the animation View repository

Motivation

What makes two cells similar?

Volume and sphericity are useful summaries, but cells with similar measurements can have very different boundaries. I wanted a way to compare surfaces directly and trace each one back to the microscopy it came from.

Implementation

Link shape back to the image

The project reconstructed 1,088 cells across 108 microscopy stacks. The viewer connects each cell’s source slices and 3D surface with measurements, embeddings, and nearest-neighbor comparisons.

Project animation

From organoid to shape atlas

Watch the reconstructed cells separate, move into a map of shapes, and reveal a query cell’s nearest matches. The motion is illustrative and the cell surfaces are reconstructed from the project’s microscopy data.

FIG. 01 One reconstructed organoid enters a preview of a UMAP embedding, then three nearby shapes are shown beside the query. Proximity in this exploratory map reflects the shape descriptors used for the embedding.

Check a comparison against the source

Linked views make it possible to select a cell in a plot and inspect its reconstructed surface and raw slices. That connection helps distinguish a genuine boundary feature from a segmentation artifact.

Organoid Atlas interface with linked scatterplots, a table of measurements, a colored 3D reconstruction, raw slices, and side-by-side cell surfaces — FIG. 02 The macOS app links plots, reconstructed surfaces, and raw microscopy. The colors in the plots indicate exploratory groups.