CellMap Project Team
- 35 followers
- United States of America
- https://www.janelia.org/project-team/cellmap
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Repositories
- cellmap-flow Public
Interactive, on-the-fly deep-learning inference and visualization for large-scale 3D microscopy data in Neuroglancer.
- mesh-n-bone Public
Generate multiresolution neuroglancer meshes and skeletons from segmentation volumes (zarr, N5, precomputed), parallelized with Dask.
- cellmap-models Public
Repository of model architectures and network weights used for CellMap segmentations.
- ask-to-mask Public
Organelle segmentation for electron microscopy with vision-language models and SAM3: VLM-guided prompting, generative image-edit masks (Flux, Gemini, Qwen), agentic refinement, and zarr/3D support.
- proofreader-mcp Public
MCP server for image-centric proofreading: rank likely-erroneous segmentation objects from per-object mesh screenshots for human review
- cellmap-analyze Public
Dask-powered tools for processing and analyzing terabyte-scale 3D segmentations: connected components, contact sites, skeletonization, measurements and more.
- CineMap Public
- cellmap-segmentation-challenge Public
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.
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