Download current and previous versions of CellPilot. We recommend using the latest version for the best experience and security updates.
| Version | Date | macOS (Intel) | macOS (Apple Silicon) | Windows | Linux | Notes |
|---|---|---|---|---|---|---|
| 2.0.2 Latest | Sep 29, 2026 | DMG | DMG | EXE | DEB | Bug-fix release |
| 2.0.1 Previous | Jul 29, 2026 | DMG | DMG | EXE | — | macOS maintenance release |
| 2.0.0 Previous | May 20, 2026 | DMG | DMG | EXE | DEB | Major CellPilot v2 update |
| 1.0.0 Previous | Jan 15, 2026 | DMG | DMG | EXE | DEB | Initial release |
MCP Server
The CellPilot MCP server connects CellPilot to AI assistants such as Claude Desktop and Codex. Downloads are .zip wrapped and install with a double-click. See the Connect via MCP tutorial for setup. Available for macOS, Windows, and Linux.
| Assistant | Version | macOS (Apple Silicon) | macOS (Intel) |
|---|---|---|---|
| Claude Desktop | 0.2.55 Latest | .mcpb | .mcpb |
| Codex | 0.2.61 Latest | Installer | Installer |
Changelog
v2.0.2 (September 29, 2026)
- Bug fixes and stability improvements
- Signed and notarized macOS builds for Intel and Apple Silicon
- Windows and Linux builds
v2.0.1 (July 29, 2026)
- Corrected marker-gene percentages for cells outside the selected cluster
- Corrected cluster-information marker statistics to use the current normalized expression matrix
- Signed and notarized macOS builds for Intel and Apple Silicon
v2.0.0 (May 20, 2026)
- Major CellPilot v2 workflow update
- Added dedicated analysis modes for scRNA-seq, scATAC-seq, and scMultiome data
- Expanded spatial analysis support for Xenium, Visium HD, MERFISH, and CosMx datasets
- Added multi-sample integration workflows for scRNA-seq, scATAC-seq, scMultiome, Xenium, and Visium HD data
- Added Agent mode for guided analysis commands and result interpretation
- Updated tutorial structure for module-specific v2 documentation
v1.0.0 (January 15, 2026)
- Initial public release
- Complete single-cell analysis pipeline
- Interactive UMAP/t-SNE visualizations
- AI-powered analysis assistant
- Support for H5 count files and 10X Cell Ranger output folders
- macOS builds for Intel and Apple Silicon
Checksums
Verify your downloads using SHA-256 checksums:
# v2.0.2 ZIP downloads
CellPilot-2.0.2.dmg.zip 3052f31990091c68d1337adc4d8eed6ad11c6aaaa6a06b35929a4c9e1fa4e0ae
CellPilot-2.0.2-arm64.dmg.zip 3b35683f062e98c0042029ec70dc50f4700ee1b5a82ab63b488821adac538655
CellPilot_2.0.2_win.zip 24061a5a679024dd0dd887fe181039f446d897d0c1da085fd111a70f32c886db
cellpilot_2.0.2_linux.zip 10d8e706a4ac011d2b3ab1f02c91435f32ec2974916c4da8b4b0870aaf0e1a13
# v2.0.1 macOS ZIP downloads
CellPilot-2.0.1.dmg.zip 8dad53fdd43dcebc1742d5656f4a7abf07003b6fa248abeba0b1a788cfb53d08
CellPilot-2.0.1-arm64.dmg.zip 250a9f672ff177af3bfb9347e91f485c5106cc5a103e96c99b98c0bae04e1153
# v2.0.0
CellPilot-2.0.0.dmg [SHA256 checksum will be added]
CellPilot-2.0.0-arm64.dmg [SHA256 checksum will be added]
# v1.0.0
CellPilot-1.0.0.dmg [SHA256 checksum will be added]
CellPilot-1.0.0-arm64.dmg [SHA256 checksum will be added]