CellMap Project Team
Using computer vision and machine learning techniques to scalably detect subcellular structures, such as organelles, in datasets generated with next-gen vEM
United States of America
Pinned Repositories
cellmap-data
Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.
cellmap-models
Repository of model architectures and network weights used for CellMap segmentations.
cosem-segmentation-analysis
Code to segment and analyze COSEM predictions
dacapo
A framework for easy application of established machine learning techniques on large, multi-dimensional images.
fibsem-tools
Tools for handling FIB-SEM data and annotations
heinrich-2021a
Resources for Heinrich et al., 2021
multiresolution-mesh-creator
openorganelle
A portal for viewing FIB-SEM datasets
pydantic-zarr
Pydantic models for Zarr
schemas
Documentation of how data, metadata, and derived data are are organized for the COSEM project
CellMap Project Team's Repositories
janelia-cellmap/dacapo
A framework for easy application of established machine learning techniques on large, multi-dimensional images.
janelia-cellmap/pydantic-zarr
Pydantic models for Zarr
janelia-cellmap/fibsem-tools
Tools for handling FIB-SEM data and annotations
janelia-cellmap/openorganelle
A portal for viewing FIB-SEM datasets
janelia-cellmap/cellmap-models
Repository of model architectures and network weights used for CellMap segmentations.
janelia-cellmap/multiresolution-mesh-creator
janelia-cellmap/cellmap-schemas
Schemas for our data
janelia-cellmap/cosem-lm-em-registration
Cosem tools for inter-modality image registration.
janelia-cellmap/ngff-zarr
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
janelia-cellmap/utils-share
Repository for sharing useful pieces of code relevant to CellMap projects
janelia-cellmap/amira_python_extensions
Extensions to Amira for reading and writing common array container formats (HDF5, N5)
janelia-cellmap/cellmap-data
Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.
janelia-cellmap/cellmap-nuclei
Generating nucleus segmentations for FIB-SEM datasets of cells and tissues
janelia-cellmap/fibsem-metadata
Human-readable descriptions of our datasets
janelia-cellmap/funlib.persistence
Interfaces for data (arrays and graphs) and storage formats (databases and file formats)
janelia-cellmap/n5-to-ome-zarr
janelia-cellmap/process-blockwise
janelia-cellmap/rusty_mws
A package for a parallelized Rust-based implementation of Mutex Watershed image segmentation, built using MongoDB and Daisy.
janelia-cellmap/annotator-metrics
janelia-cellmap/openorganelle-blog
Periodic content for openorganelle
janelia-cellmap/airtable-backups
Configurable automated backups for Airtable
janelia-cellmap/combine-amira-tifs
Fiji script to combine segmentation tifs from amira such that unique ids are kept
janelia-cellmap/converter
A tool for converting files from one format to another.
janelia-cellmap/expr_c-elegans
janelia-cellmap/funlib.evaluate
janelia-cellmap/neuroglancer
WebGL-based viewer for volumetric data
janelia-cellmap/neuroglancer-url-tools
Typescript objects for synthesizing URLs for the neuroglancer visualization tool.
janelia-cellmap/nuclear_pore_setup
Nuclear pore preprocessing and set up for the CellMap Project at Janelia for the Janelia-Meyerhoff Undergraduate Program
janelia-cellmap/pycookie
A cookie cutter repository for python projects.
janelia-cellmap/pydantic-neuroglancer
Pydantic models for Neuroglancer