Celldega: Spatial Analysis and Visualization Library

Broad Retreat 2024
Data Visualization Breakout Session
Spatial Technology Platform

Nicolas Fernandez
@cornhundred.bsky.social

Motivation

The cell is the fundamental unit of life

Cells differentiate and work together to form intricately organized:

  • tissues
  • organs
  • organisms

Enabled by the careful regulation of transcriptional programs

Spatial Transcriptomics

Single-cell transcriptomics reveals the high-dimensional gene expression space that cells reside in

Spatial techniques reveal where cells are located in physical space

First Image Description Second Image Description

Celldega: Xenium Prime Mouse Brain Coronal FF

Celldega: Xenium Prime Human Skin Cancer

Acknowledgements

Sami Farhi
Lindsey Erion-Barner
Michal Lipinski
Huan Wang
Jaspreet Ishar
Keisha Matthew
Sara Sime
Sachi Krishna
Jack Nelson
Brad Tremblay
Tamara Aleksanyan
Gunjan Jetley
Ari Koplowitz
Loïc Binan
Vy Ngo
Jax Xu
Alec Barrios
Peter Bryan
Sartaj Habib
Byunguk Kang
Darian Ventura

Links

Spatial Technology Platform
broadinstitute.org/spatial-technology-platform
@stp-broad.bsky.social
Celldega
github.com/broadinstitute/celldega
broadinstitute.github.io/Celldega-Broad-Retreat-2024