CellMap Project Team's repositories
pydantic-zarr
Pydantic models for Zarr
fibsem-tools
Tools for handling FIB-SEM data and annotations
openorganelle
A portal for viewing FIB-SEM datasets
cellmap-models
Repository of model architectures and network weights used for CellMap segmentations.
cellmap-schemas
Schemas for our data
cosem-lm-em-registration
Cosem tools for inter-modality image registration.
utils-share
Repository for sharing useful pieces of code relevant to CellMap projects
amira_python_extensions
Extensions to Amira for reading and writing common array container formats (HDF5, N5)
cellmap-data
Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.
cellmap-nuclei
Generating nucleus segmentations for FIB-SEM datasets of cells and tissues
fibsem-metadata
Human-readable descriptions of our datasets
funlib.persistence
Interfaces for data (arrays and graphs) and storage formats (databases and file formats)
openorganelle-blog
Periodic content for openorganelle
airtable-backups
Configurable automated backups for Airtable
combine-amira-tifs
Fiji script to combine segmentation tifs from amira such that unique ids are kept
neuroglancer
WebGL-based viewer for volumetric data
neuroglancer-url-tools
Typescript objects for synthesizing URLs for the neuroglancer visualization tool.
nuclear_pore_setup
Nuclear pore preprocessing and set up for the CellMap Project at Janelia for the Janelia-Meyerhoff Undergraduate Program
pycookie
A cookie cutter repository for python projects.
pydantic-neuroglancer
Pydantic models for Neuroglancer