Image reading, metadata management, and image writing for Microscopy images in Python

Napari plugin to ease manual correction of epithelial movie segmentation

A tool for cell instance aware segmentation in densely packed 3D volumetric images

nextflow module/subworkflow for image deconvolution

A compute graph for loading and transforming OWID's data

GPU-accelerated template matching for cryo-ET

Official implementation of MuViT (CVPR 2026), a ViT-based architecture for multi-scale modelling of gigapixel microscopy images.

Run pytest on markdown code fence blocks

PyTorch Single Controller

Unified API for streaming camera frames to either OME-TIFF or OME-Zarr format

Equivariant Steerable CNNs Library for Pytorch https://quva-lab.github.io/escnn/

Block-wise task scheduling for large nD volumes.

A modern static site generator by the Material for MkDocs team

A CodecPipeline for zarr-python backed by the zarrs Rust crate

Official PyTorch implementation of the "SN2N"

Pydantic models for the TensorStore Spec

Accurate and efficient spot detection for microscopy data

Create, manage, and run Jupyter notebooks with their dependencies

Ngio is a Python library to streamline OME-Zarr image analysis workflows.

Transformer-based cell tracking for live-cell microscopy

A local-first personal finance app

Morphological profiling using deep learning

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…

A highly customizable and improved version of Carmine Spagnuolo's Twenty Seconds Curriculum Vitae.

Deeplay is a deep learning library in Python that extends PyTorch with additional functionalities focused on modularity and reusability.

Utility for visualizing results on the fly in neuroglancer

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

🎀 Awesome Zarr resources

Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.