Repositories list

• cellmap-data

  Public
  Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.

  machine-learningndarraydataloader+ 1zarr

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2•6•4•2•Updated Nov 27, 2025Nov 27, 2025

• cellmap-segmentation-challenge

  Public
  Repository of scripts to facilitate participation in CellMap's segmentation challenge. This includes downloading data, simple setups for training 2D and 3D models, workflows for prediction and post-processing on out-of-memory arrays, and evaluation of results against validation data.

  machine-learningbiologyartificial-intelligence+ 3segmentationzarrome-ngff

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •14•39•8•3•Updated Nov 25, 2025Nov 25, 2025

• cellmap-analyze

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•0•Updated Nov 20, 2025Nov 20, 2025

• igneous-daskified

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•3•0•0•Updated Nov 20, 2025Nov 20, 2025

• LeibNetz

  Public
  A lightweight and modular library for rapidly developing and constructing PyTorch models deep learning.

  machine-learningcnnpytorch

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•1•1•Updated Nov 17, 2025Nov 17, 2025

• exp-overview

  Public
  an overview and reference for the experimental projects

  HTML

  •0•1•0•0•Updated Nov 12, 2025Nov 12, 2025

• cellmap-flow

  Public
  Utility for visualizing results on the fly in neuroglancer

  machine-learningsegmentationneuroglancer

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•7•5•5•Updated Oct 21, 2025Oct 21, 2025

• zarrify

  Public
  A simple tool to convert datasets stored in different image formats to zarr array

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•1•0•Updated Oct 20, 2025Oct 20, 2025

• metabolic-liver-zonation

  Public
  Analysis code and workflows for mapping organelle architecture across liver zonation using FIB-SEM. Includes tools for ER–mitochondria contact quantification, morphometrics, and zone-aware analysis. Designed for reproducible, modular exploration of metabolic ultrastructure.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Oct 14, 2025Oct 14, 2025

• dacapo

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

  machine-learningdeep-learningsegmentation

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •10•60•23•7•Updated Sep 15, 2025Sep 15, 2025

• zarr-fractional-rescale

  Public
  Python

  •0•0•0•0•Updated Sep 3, 2025Sep 3, 2025

• frx-challenges

  Public
  Welcome to Janelia's fork of the FRX Challenges project! This is an open source repository that provides key software components for running competitive data science challenges. FRX stands for Frictionless Reproducibility eXchange. Inspired by Donoho, 2023. This project enables communities to host data challenges with live evaluation.

  CSS

  •

  BSD 3-Clause "New" or "Revised" License

  •5•1•0•0•Updated Aug 22, 2025Aug 22, 2025

• zarr-multiscale

  Public
  Python

  •0•1•0•0•Updated Aug 15, 2025Aug 15, 2025

• multiresolution-mesh-creator

  Public
  Python

  •

  Other

  •2•9•1•1•Updated Jul 30, 2025Jul 30, 2025

• openorganelle

  Public
  A portal for viewing FIB-SEM datasets

  TypeScript

  •

  Other

  •3•11•26•4•Updated Jun 26, 2025Jun 26, 2025

• dacapo-cellmap-config

  Public
  dacapo Cellmap Related tools

  Python

  •0•0•0•0•Updated Jun 9, 2025Jun 9, 2025

• openorganelle-blog

  Public
  Periodic content for openorganelle

  BSD 3-Clause "New" or "Revised" License

  •2•0•5•0•Updated Apr 11, 2025Apr 11, 2025

• fibsem-tools

  Public
  Tools for handling FIB-SEM data and annotations

  Python

  •

  MIT License

  •8•22•9•3•Updated Apr 4, 2025Apr 4, 2025

• amira_python_extensions

  Public
  Extensions to Amira for reading and writing common array container formats (HDF5, N5)

  Batchfile

  •2•1•0•0•Updated Mar 26, 2025Mar 26, 2025

• cellmap-models

  Public
  Repository of model architectures and network weights used for CellMap segmentations.

  machine-learningsegmentation

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•13•1•0•Updated Jan 15, 2025Jan 15, 2025

• cellmap-n5-to-zarr

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• process-blockwise

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•1•0•Updated Jan 10, 2025Jan 10, 2025

• n5_to_ome_zarr

  Public
  This program converts a .n5 file into a .zarr file with ome-ngff multiscale metadata .zattrs file

  Python

  •0•3•0•0•Updated Jan 7, 2025Jan 7, 2025

• mrc-to-zarr

  Public
  Convert large mrc files to zarr arrays

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•3•0•0•Updated Nov 6, 2024Nov 6, 2024

• cellmap-schemas

  Public
  Schemas for our data

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•2•1•1•Updated Oct 18, 2024Oct 18, 2024

• annotator-metrics

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated Oct 13, 2024Oct 13, 2024

• rusty_mws

  Public
  A package for a parallelized Rust-based implementation of Mutex Watershed image segmentation, built using MongoDB and Daisy.

  Python

  •

  Apache License 2.0

  •2•1•0•1•Updated Sep 17, 2024Sep 17, 2024

• expr_c-elegans

  Public archive
  Python

  •0•0•0•0•Updated Aug 1, 2024Aug 1, 2024

• neuroglancer

  Public
  WebGL-based viewer for volumetric data

  TypeScript

  •

  Apache License 2.0

  •334•0•0•0•Updated Jul 23, 2024Jul 23, 2024

• cellmap-nuclei

  Public
  Generating nucleus segmentations for FIB-SEM datasets of cells and tissues

  BSD 3-Clause "New" or "Revised" License

  •0•1•30•0•Updated Jul 2, 2024Jul 2, 2024