Highly automated AI workflows for single-cell analysis in time-lapse microscopy

Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.

Config files for microscopes of the pertzlab, university of Bern

Visualize, share and annotate your large 3D images online

Reference PyTorch implementation and models for DINOv3

Agent Reinforcement Trainer: train multi-step agents for real-world tasks using GRPO. Give your agents on-the-job training. Reinforcement learning for Qwen2.5, Qwen3, Llama, and more!

Smart microscopy library at LEB EPFL

This repository contains the code to fit a biological model (ODE system) to the experimental data of RhoA activity obtained by Heydasch et al. (2023) for their research.

interactive & hardware agnostic SDK for lab automation

[NeurIPS 2025] Official code for JAFAR: Jack up Any Feature at Any Resolution

Cellular Agent-based Modeling from a Clean Slate

Scientific Inkscape: Inkscape extensions for figure resizing and editing

Scientific colormaps for python, with only numpy dependency

A library for computational imaging with the Enderscope

Segment images utilizing pre-trained neural networks as feature extractors

Real-time feedback control microscopy using pymmcore as interface

An R package to detect collective spatio-temporal phenomena

A napari plugin to track spatio-temporal correlations in images

This repository provides DINOSim, a method that leverages the DINOv2 foundation model for zero-shot object detection and segmentation in bioimage analysis. DINOSim uses pretrained DINOv2 embeddings…

This repository is a toolset for microscope that use pymmcore-plus with LLM

2D and 3D grayscale orientation analysis in Napari.

litemind is a Python library designed to empower developers to build sophisticated conversational agents and tools. It provides a flexible and elegant API for interacting with Large Language Models…

An implementation agnostic schema for describing a sequence of events during a multi-dimensional imaging acquisition.

The official Python SDK for Model Context Protocol servers and clients

Loading and handling microscopy data in blender