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CellPilot 2.0.1 for macOS Released

July 29, 2026

CellPilot 2.0.1 is now available for Intel and Apple Silicon Macs. This maintenance release corrects marker-gene detection percentages and cluster-information marker statistics.

  • Corrected pct.2 values for expression outside the selected cluster.
  • Marker summaries now use the current normalized expression matrix.
  • Both macOS builds are signed and notarized by Apple.

Download CellPilot 2.0.1 for macOS.

CellPilot MCP for Claude and Codex

June 18, 2026

CellPilot now offers an MCP (Model Context Protocol) server so you can connect it to external AI assistants. Install it once and Claude Desktop or Codex can call CellPilot's analysis tools for you through natural language.

  • Builds for Claude Desktop (a .mcpb bundle) and Codex (a .dmg installer).
  • One-step, double-click install with no terminal or config editing.
  • Connects to the installed desktop apps, not the web versions.
  • Available for macOS (Apple Silicon and Intel), Windows, and Linux.

Download from the Download page and follow the Connect via MCP tutorial.

CellPilot 2.0.0 Released

May 20, 2026

CellPilot is now a no-code platform for single-cell, chromatin accessibility, multiome, spatial, integration, and agent-guided analysis.

Highlights

  • scRNA-seq, scATAC-seq, and scMultiome analysis tutorials and workflows.
  • Spatial analysis support for Xenium, Visium HD, MERFISH, and CosMx.
  • Multi-sample integration workflows for scRNA-seq, scATAC-seq, multiome, and spatial datasets.
  • WNN integration for paired multiome RNA and ATAC data.
  • Histology image overlay workflows for Xenium and Visium HD when alignment information is available.
  • Selected spatial region marker analysis and region interpretation.
  • Cell-cell interaction analysis across multiple selected spatial regions.
  • Agent Mode for multi-step analysis planning, cluster annotation, selected-region annotation, and result interpretation.
  • Updated tutorial hub with workflow-specific pages for CellPilot.

Initial Public Release

January 15, 2026

The first public release introduced CellPilot for no-code single-cell analysis.

Initial features:

  • Single-cell RNA analysis pipeline
  • Interactive UMAP and t-SNE visualizations
  • Chat-assisted analysis commands
  • Support for H5 count files and 10x Cell Ranger output folders
  • Local computation on the user's machine

For download history, see the Release Archive. Follow development on GitHub.