Name: CellMap Project Team
Type: Organization
Bio: Using computer vision and machine learning techniques to scalably detect subcellular structures, such as organelles, in datasets generated with next-gen vEM
Location: United States of America
Blog: https://www.janelia.org/project-team/cellmap
CellMap Project Team's Projects
Configurable automated backups for Airtable
Extensions to Amira for reading and writing common array container formats (HDF5, N5)
Metadata for annotations
Materials pursuant to our entry in the AWS Open Data program
CellMap hackathon blog
Repository of model architectures and network weights used for CellMap segmentations.
Schemas for our data
AWS CDK stacks for cellmap.
Fiji script to combine segmentation tifs from amira such that unique ids are kept
A tool for converting files from one format to another.
Java tools
Config files for setting up a database for tracking COSEM datasets
Cosem tools for inter-modality image registration.
Code to segment and analyze COSEM predictions
Tutorials, how-tos, and demonstrations.
Various notebooks for one-off operations
A framework for easy application of established machine learning techniques on large, multi-dimensional images.
Align FIB SEM stacks on a cluster
Human-readable descriptions of our datasets
Repository related to optical flow calculations for fibsem images
Tools for handling FIB-SEM data and annotations
Interfaces for data (arrays and graphs) and storage formats (databases and file formats)
Resources for Heinrich et al., 2021