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    • Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.
      Python
      BSD 3-Clause "New" or "Revised" License
      1261Updated Dec 23, 2024Dec 23, 2024
    • 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.
      Python
      BSD 3-Clause "New" or "Revised" License
      11771Updated Dec 23, 2024Dec 23, 2024
    • A portal for viewing FIB-SEM datasets
      TypeScript
      Other
      311234Updated Dec 19, 2024Dec 19, 2024
    • Periodic content for openorganelle
      BSD 3-Clause "New" or "Revised" License
      2050Updated Dec 16, 2024Dec 16, 2024
    • Python
      BSD 3-Clause "New" or "Revised" License
      0000Updated Dec 13, 2024Dec 13, 2024
    • dacapo

      Public
      A framework for easy application of established machine learning techniques on large, multi-dimensional images.
      Python
      BSD 3-Clause "New" or "Revised" License
      9492613Updated Dec 10, 2024Dec 10, 2024
    • Python
      BSD 3-Clause "New" or "Revised" License
      0000Updated 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
      0130Updated Nov 13, 2024Nov 13, 2024
    • Convert large mrc files to zarr arrays
      Python
      BSD 3-Clause "New" or "Revised" License
      0100Updated Nov 6, 2024Nov 6, 2024
    • This program converts a .n5 file into a .zarr file with ome-ngff multiscale metadata .zattrs file
      Python
      0300Updated Nov 4, 2024Nov 4, 2024
    • Repository of model architectures and network weights used for CellMap segmentations.
      Python
      BSD 3-Clause "New" or "Revised" License
      01010Updated Oct 24, 2024Oct 24, 2024
    • Schemas for our data
      Python
      BSD 3-Clause "New" or "Revised" License
      1211Updated Oct 18, 2024Oct 18, 2024
    • Python
      MIT License
      1000Updated 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
      2101Updated Sep 17, 2024Sep 17, 2024
    • Tools for handling FIB-SEM data and annotations
      Python
      MIT License
      82193Updated Sep 16, 2024Sep 16, 2024
    • Python
      Other
      2400Updated Aug 7, 2024Aug 7, 2024
    • Python
      BSD 3-Clause "New" or "Revised" License
      0110Updated Aug 5, 2024Aug 5, 2024
    • Python
      0000Updated Aug 1, 2024Aug 1, 2024
    • WebGL-based viewer for volumetric data
      TypeScript
      Apache License 2.0
      299000Updated Jul 23, 2024Jul 23, 2024
    • Generating nucleus segmentations for FIB-SEM datasets of cells and tissues
      BSD 3-Clause "New" or "Revised" License
      01300Updated Jul 2, 2024Jul 2, 2024
    • Repository for sharing useful pieces of code relevant to CellMap projects
      Python
      0200Updated Jun 25, 2024Jun 25, 2024
    • Extensions to Amira for reading and writing common array container formats (HDF5, N5)
      Batchfile
      2100Updated Jun 17, 2024Jun 17, 2024
    • Interfaces for data (arrays and graphs) and storage formats (databases and file formats)
      Python
      MIT License
      10100Updated Apr 16, 2024Apr 16, 2024
    • pycookie

      Public
      A cookie cutter repository for python projects.
      Python
      2000Updated Apr 2, 2024Apr 2, 2024
    • Fiji script to combine segmentation tifs from amira such that unique ids are kept
      MIT License
      0000Updated Mar 12, 2024Mar 12, 2024
    • Pydantic models for Neuroglancer
      Python
      1000Updated Oct 6, 2023Oct 6, 2023
    • Python
      MIT License
      7000Updated 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
      4200Updated Sep 26, 2023Sep 26, 2023
    • Configurable automated backups for Airtable
      TypeScript
      10000Updated Jul 26, 2023Jul 26, 2023
    • Nuclear pore preprocessing and set up for the CellMap Project at Janelia for the Janelia-Meyerhoff Undergraduate Program
      Jupyter Notebook
      0000Updated Jun 8, 2023Jun 8, 2023