Stars
A Python toolbox for aligning / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
Chemomechanical model of avian hindgut formation, written in FEniCS (Python)
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
This repository contains the code used to generate the results presented in "Data-driven identification of biomedical systems using multi-scale analysis". The toolkit integrates methods for sparse …
CUDA-accelerated 3D BioImage Computing (ICCV BIC 2025)
Optimal transport tools implemented with the JAX framework, to solve large scale matching problems of any flavor.
A basis for a napari plugin for manually correcting cell segmentation in 3D (z, y, x) or 4D (t, z, y, x) (virtual) arrays.
Code associated with: A toolkit for mapping cell identities in relation to neighbours reveals conserved patterning of neuromesodermal progenitor populations.
Utilities for computing common accuracy metrics on cell tracking solutions with ground truth
LLM-powered personalized daily lists of scientific papers
Extract surfaces from 3D microscopy images and project them to 2D for analysis and visualization
Utility code to generate kymorgraph plots from nD images, compatible with napari
Algorithms for identifying coherent structures in sparse and noisy trajectory datasets
Analysis of junctional protein localization patterns in epithelial tissues
The 2025 version of cellPLATO
A collection of useful python utilities from True North Intelligent Algorithms
ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy