Welcome to Celldega's Documentation
Celldega is a spatial analysis and visualization library that is being developed by the Spatial Technology Platform at the Broad Institute of MIT and Harvard. This project enables researchers to easily visualize large ST datasets (e.g., datasets with >100M transcripts) alongside single-cell and spatial analysis notebook workflows (e.g., sverse tools and novel spatial analysis approaches).
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. See the Broad-Allen Dev Mouse Brain E15.5 Viz tutorial.
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.