Projects
We develop open-source tools for image registration, spatial transcriptomics, organoid analysis, and cell lineage handling. All software is freely available on GitHub.
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A fully-visual pipeline for quantitative analysis of 3D organoid images from deep imaging microscopy.
A library for manipulating and analyzing 3D spatial transcriptomics data at near single-cell resolution.
A library to register 3D movies in space and/or time, enabling alignment of live-imaging datasets.
A napari viewer designed for interactive exploration of 3D spatial transcriptomics data.
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A napari plugin providing a graphical interface for the registration-tools library.
A library to handle, manipulate, and analyse cell lineage trees from time-lapse imaging.
Automated cell detection and tracking algorithm for whole-embryo light-sheet imaging data.
A computational library implementing Statistical Vector Flow for morphological atlas construction.
Standalone implementation of the tracking code from McDole et al. 2018 (Cell).
Computational model simulating cell-cell signaling interactions during embryogenesis.
Educational resource teaching Python programming through Turing-model simulations of biological patterns.