jdeschamps

AreTomo2

ndv

Simple, fast-loading, n-dimensional array viewer with minimal dependencies.

psygnal

Python observer pattern (callback/event system). Modeled after Qt Signals & Slots (but independent of Qt)

numpydantic

Type and shape validation and serialization for numpy arrays in pydantic models

featureforest

A napari plugin for segmentation using vision transformers' features

mike

Manage multiple versions of your MkDocs-powered documentation via Git

suite2p

cell detection in calcium imaging recordings

sybil

Automated testing for the examples in your documentation.

benchmark_VAE

Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

i2kconference

I2K Conference Website

faim-ipa

A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)

sofima

Scalable Optical Flow-based Image Montaging and Alignment

shellcheck

ShellCheck, a static analysis tool for shell scripts

mlf-core

CPU and GPU deterministic and therefore fully reproducible machine learning pipelines using MLflow.

ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

pyxu

Modular and scalable computational imaging in Python with GPU/out-of-core computing.

CebraEM

ome-zarr-image-analysis-nextflow

Basic example of using OME-Zarr in a Nextflow pipeline

Next-Generation-File-Format-Features

This repository is a proposal for addin generalistic feature specs in the context of the next generation bioimage analysis workflows hackathon 2023

msgspec

A fast serialization and validation library, with builtin support for JSON, MessagePack, YAML, and TOML

ome-zarr-py

Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

BiaPy

Open source Python library for building bioimage analysis pipelines

schemas

Documentation of how data, metadata, and derived data are are organized for the COSEM project

tensorstore

Library for reading and writing large multi-dimensional arrays.

pydantic-zarr

Pydantic models for Zarr

nextflow-examples

zarrdataset

A dataset for loading zarr files to be used in machine learning training pipelines

cookie

Scientific Python Library Development Guide and Cookiecutter

torch-em

Deep-learning based semantic and instance segmentation for 3D Electron Microscopy and other bioimage analysis problems based on pytorch.