A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.

A framework for easy application of established machine learning techniques on large, multi-dimensional images.

Documentation page

Bayesian multi-object tracking

napari plugin for trackastra

Small library for analysis of mother machine data. Built to run on a SLURM cluster, but can be run locally.

A JAX research toolkit for building, editing, and visualizing neural networks.

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

Multi-Object Tracker using Integer Linear Equations

Drag and drop images to Emacs org-mode

An ImageJ/Fiji plugin designed to effortlessly integrate Segment-Anything models (SAMs) without code.

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

Everything to get started with computer vision

Accurate and efficient spot detection for microscopy data

Bayesian Segmentation of Spatial Transcriptomics Data

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

🎈 Simple reactive notebooks for Julia

RIVET is a tool for Topological Data Analysis, in particular two-parameter persistent homology.

A high-performance topological machine learning toolbox in Python

Goo is a Blender library for modeling biological cells, tissues, and embryos

personal scientific website

DeepTrack2 is a modular Python library for generating, manipulating, and analyzing image data pipelines for machine learning and experimental imaging.

Segment Anything for Microscopy

An open and interoperable data framework for spatial omics data

Website and blog generator for Go, Node.js or Python