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@janelia-cellmap CellMap Project Team

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    64 repositories

    • cellmap-data

      Public
      Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.
      machine-learningndarraydataloaderzarr
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•8•0•Updated Jan 10, 2025Jan 10, 2025

    • cellmap-n5-to-zarr

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 10, 2025Jan 10, 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-intelligencesegmentationzarrome-ngff
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•17•8•1•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

    • 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•49•23•6•Updated Jan 9, 2025Jan 9, 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•11•1•0•Updated Jan 9, 2025Jan 9, 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

    • openorganelle

      Public
      A portal for viewing FIB-SEM datasets
      TypeScript
      •
      Other
      •3•11•23•4•Updated Jan 3, 2025Jan 3, 2025

    • csc-experiments

      Public
      This repository contains the code for the experiments conducted by the CellMap Project Team in order to establish baseline performance metrics for the CellMap Segmentation Challenge.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 2, 2025Jan 2, 2025

    • openorganelle-blog

      Public
      Periodic content for openorganelle
      BSD 3-Clause "New" or "Revised" License
      •2•0•5•0•Updated Dec 16, 2024Dec 16, 2024

    • segmentation-challenge-meshes

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 13, 2024Dec 13, 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•2•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

    • 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

    • 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
      •300•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
      •11•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