Welcome to Celldega's Documentation
Celldega is a spatial and single-cell analysis and visualization library developed by the Spatial Technology Platform at the Broad Institute of MIT and Harvard. Explore large spatial datasets, including datasets with over 1 billion transcripts, and single-cell atlases with over a million cells, alongside analysis workflows using scverse tools such as Scanpy and Squidpy.
What's New
Atera
Visualize 10x Atera whole-transcriptome data in Celldega. The Atera Kidney Landscape-Clustergram tutorial explores 399,120 cells and over 1 billion transcripts in a human kidney section with linked Landscape, Clustergram, and Yearbook views, including cell-type composition around glomeruli.
Visium HD Colorectal Cancer Tutorial Video
This video shows how to link a Landscape, Clustergram, and Enrich to analyze a Visium HD human colorectal cancer dataset. Follow along in the Visium HD Human CRC Landscape-Clustergram-Enrich tutorial.
3D Developing Mouse Brain
Explore 3.8 million cells from 43 aligned Xenium sections of an E15.5 mouse brain as a 3D CellCloud. Open the interactive CellCloud gallery using compact Parquet DegaFiles, or follow the visualization notebook using AnnData Zarr on Hugging Face to link CellCloud with a Clustergram.
bioRxiv Preprint
Our preprint, Celldega: Integrated Toolkit for Visualization and Analysis of Spatial Data, is available on bioRxiv.
About
Celldega is named after a bodega, a small shop with all the essentials that is part of the fabric of a neighborhood.
Celldega is open source and available on GitHub.