CellMap Project Team

dacapo

A framework for easy application of established machine learning techniques on large, multi-dimensional images.

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.

multiresolution-mesh-creator

cellmap-schemas

Schemas for our data

cosem-lm-em-registration

Cosem tools for inter-modality image registration.

ngff-zarr

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

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)

n5-to-ome-zarr

process-blockwise

rusty_mws

A package for a parallelized Rust-based implementation of Mutex Watershed image segmentation, built using MongoDB and Daisy.

openorganelle-blog

Periodic content for openorganelle

airtable-backups

Configurable automated backups for Airtable

annotator-metrics

combine-amira-tifs

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

converter

A tool for converting files from one format to another.

expr_c-elegans

funlib.evaluate

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