Software

We develop open-source tools for image registration, spatial transcriptomics, organoid analysis, and cell lineage handling.

All software is open source available on GitHub.

Featured

Tapenade 3D organoid image analysis

A fully-visual pipeline for quantitative analysis of 3D organoid images from deep imaging microscopy.

sc3D 3D spatial transcriptomics

A library for manipulating and analyzing 3D spatial transcriptomics data at near single-cell resolution.

registration-tools 3D movie registration

A library to register 3D movies in space and/or time, enabling alignment of live-imaging datasets.

napari-sc3D-viewer napari plugin

A napari viewer designed for interactive exploration of 3D spatial transcriptomics data.

LineageTree Cell lineage handling

A library to handle, manipulate, and analyse cell lineage trees from time-lapse imaging.

napari-3D-registration napari plugin

A napari plugin providing a graphical interface for the registration-tools library.

ASTEC Cell detection & tracking

Automated cell detection and tracking algorithm for whole-embryo light-sheet imaging data.

napari-obj napari plugin

A napari plugin for loading and displaying .obj 3D mesh files.

CenTuri Course Python via Turing models

Educational resource teaching Python programming through Turing-model simulations of biological patterns.