Cellucid#

Interactive Single-Cell Data Visualization

Cellucid is a GPU-accelerated, browser-first single-cell viewer for exploring massive datasets in real time — fly through 2D/3D embeddings, color by genes or metadata, filter and compare populations, and share reproducible annotations with collaborators.

Cellucid App

Features#

  • GPU-accelerated 2D/3D rendering - Smooth navigation through millions of cells

  • Genes + metadata overlays - Fast coloring for sparse/dense expression and obs fields

  • Filtering + selection workflows - Highlight, subset, and compare populations interactively

  • Connectivity + vector overlays - KNN edges and velocity/drift-style fields

  • Shareable exports - Static folders you can host locally, on GitHub, or behind a server

  • Works everywhere - Web app, local server mode, and Jupyter notebook embedding

User Guide#

Step-by-step tutorials to get you started with Cellucid visualization.

Web App

Viewer basics, filtering, highlighting, analysis, figure export, sessions, performance, and troubleshooting.

Web App Guide
Python Package

Installation, data prep, prepare()/export, viewing modes, notebook integration, hooks/events, and troubleshooting.

Python Package Guide
R Export (Preview)

Exporting data with cellucid-r (Seurat/SCE recipes) into the same format used by the Cellucid web app.

R Package Guide

Installation#

Python:

pip install cellucid

R (export package):

install.packages("remotes")
remotes::install_github("theislab/cellucid-r")