Repositories list

• 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

  •1•17•8•1•Updated Dec 20, 2024Dec 20, 2024

• openorganelle

  Public
  A portal for viewing FIB-SEM datasets

  TypeScript

  •

  Other

  •3•11•23•4•Updated Dec 19, 2024Dec 19, 2024

• openorganelle-blog

  Public
  Periodic content for openorganelle

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

  •2•0•5•0•Updated Dec 16, 2024Dec 16, 2024

• 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

  •1•1•6•1•Updated Dec 13, 2024Dec 13, 2024

• segmentation-challenge-meshes

  Public
  Python

  •

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

  •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• 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

  •9•49•26•13•Updated Dec 10, 2024Dec 10, 2024

• cellmap-n5-to-zarr

  Public
  Python

  •

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

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• LeibNetz

  Public
  A collection of existing and custom built models for use with cellmap-train and other ML training pipelines.

  Python

  •

  MIT License

  •0•1•3•0•Updated Nov 13, 2024Nov 13, 2024

• mrc-to-zarr

  Public
  Convert large mrc files to zarr arrays

  Python

  •

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

  •0•1•0•0•Updated Nov 6, 2024Nov 6, 2024

• 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 Nov 4, 2024Nov 4, 2024

• 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•9•1•0•Updated Oct 24, 2024Oct 24, 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

• fibsem-tools

  Public
  Tools for handling FIB-SEM data and annotations

  Python

  •

  MIT License

  •8•21•9•3•Updated Sep 16, 2024Sep 16, 2024

• multiresolution-mesh-creator

  Public
  Python

  •

  Other

  •2•4•0•0•Updated Aug 7, 2024Aug 7, 2024

• process-blockwise

  Public
  Python

  •

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

  •0•1•1•0•Updated Aug 5, 2024Aug 5, 2024

• expr_c-elegans

  Public
  Python

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

• neuroglancer

  Public
  WebGL-based viewer for volumetric data

  TypeScript

  •

  Apache License 2.0

  •299•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

• utils-share

  Public
  Repository for sharing useful pieces of code relevant to CellMap projects

  Python

  •0•2•0•0•Updated Jun 25, 2024Jun 25, 2024

• amira_python_extensions

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

  Batchfile

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

• funlib.persistence

  Public
  Interfaces for data (arrays and graphs) and storage formats (databases and file formats)

  Python

  •

  MIT License

  •10•1•0•0•Updated Apr 16, 2024Apr 16, 2024

• pycookie

  Public
  A cookie cutter repository for python projects.

  Python

  •2•0•0•0•Updated Apr 2, 2024Apr 2, 2024

• combine-amira-tifs

  Public
  Fiji script to combine segmentation tifs from amira such that unique ids are kept

  MIT License

  •0•0•0•0•Updated Mar 12, 2024Mar 12, 2024

• pydantic-neuroglancer

  Public
  Pydantic models for Neuroglancer

  Python

  •1•0•0•0•Updated Oct 6, 2023Oct 6, 2023

• funlib.evaluate

  Public
  Python

  •

  MIT License

  •7•0•0•0•Updated Sep 26, 2023Sep 26, 2023

• ngff-zarr

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

  Python

  •

  MIT License

  •4•2•0•0•Updated Sep 26, 2023Sep 26, 2023

• airtable-backups

  Public
  Configurable automated backups for Airtable

  TypeScript

  •10•0•0•0•Updated Jul 26, 2023Jul 26, 2023

• nuclear_pore_setup

  Public
  Nuclear pore preprocessing and set up for the CellMap Project at Janelia for the Janelia-Meyerhoff Undergraduate Program

  Jupyter Notebook

  •0•0•0•0•Updated Jun 8, 2023Jun 8, 2023