General Questions
What is CellPilot?
CellPilot is a no-code desktop application for single-cell, multiome, and spatial omics analysis. It supports scRNA-seq, scATAC-seq, scMultiome, Xenium, Visium HD, MERFISH, CosMx, integration workflows, and Agent Mode.
Is CellPilot free to use?
Yes! CellPilot is completely free for academic use. For commercial use, please contact WashU OTM (https://otm.wustl.edu/).
What platforms does CellPilot support?
CellPilot is available for macOS, Windows, and Linux.
Data & Privacy
Is my data uploaded to any server?
Core analysis runs locally on your computer. If you use Agent Mode with an API provider, CellPilot sends the user request, dataset context, and summarized analysis results needed for the agent response to the selected provider. Raw count matrices are not sent to the agent provider.
What file formats are supported?
CellPilot supports 10x Cell Ranger H5 and MatrixMarket folders, Cell Ranger ATAC folders, Cell Ranger ARC multiome folders, Space Ranger / Visium HD outputs, Xenium outputs, Vizgen MERSCOPE MERFISH outputs, and CosMx outputs.
Do I need to rename files from my own experiment?
Usually no. CellPilot is designed to accept standard output folders from Cell Ranger, Cell Ranger ATAC, Cell Ranger ARC, Space Ranger, Xenium, MERSCOPE, and CosMx/AtoMx. Some tutorials include command-line renaming only because public demo downloads often include sample IDs in every filename.
What is the maximum dataset size?
The practical limit depends on memory, modality, and workflow. Large Visium HD datasets use sketch-based analysis for responsive UMAP and clustering. For very large spatial or ATAC datasets, more RAM is recommended.
Analysis
What analysis methods are available?
CellPilot includes QC, filtering, normalization, PCA, UMAP, clustering, marker detection, gene plots, violin plots, dot plots, ATAC TF-IDF/LSI, gene activity, coverage plots, peak-gene linking for multiome, WNN integration, MNN and Harmony-based integration workflows, spatial region markers, BANKSY region segmentation, and cell-cell interaction analysis for selected spatial regions.
Can I customize the analysis parameters?
Yes. You can adjust many parameters from chat, including filtering thresholds, UMAP settings, clustering resolution, and modality-specific RNA or ATAC settings.
How does the AI assistant work?
CellPilot has multiple chat modes. Intent mode routes common commands quickly. Local AI mode can use a configured local model. Agent Mode uses an API provider such as Gemini, ChatGPT, Claude, Groq, or OpenRouter to plan multi-step analysis, annotate clusters, interpret selected spatial regions, and summarize cell-cell interaction results.
What can Agent Mode do?
Agent Mode can annotate one cluster or all clusters, find clusters matching a requested cell type, interpret a selected spatial region, run cell-cell interaction analysis across multiple selected spatial regions, and plan multi-step CellPilot tool calls. It may ask for confirmation before expensive or object-changing actions.
MCP & AI Assistant Integration
What is the CellPilot MCP server?
It is a connector that lets an external AI assistant, such as Claude Desktop or Codex, call CellPilot's analysis tools through natural language. After connecting, you can ask the assistant to load data, run workflows, and interpret results, and it invokes the matching CellPilot tools for you. See the Connect via MCP tutorial.
Do I need the desktop app or the web app?
The desktop app. MCP connects to the installed Claude Desktop or Codex application, not the website. Install Claude Desktop from claude.ai/download, or the Codex desktop/CLI tooling from OpenAI. The browser versions cannot load the MCP server.
How do I install the MCP?
It is a double-click install with no terminal or config editing. Download the build for your assistant from the Download page, unzip it, then double-click the .mcpb bundle (Claude) or run the .dmg installer (Codex). Full steps are in the Connect via MCP tutorial.
Which MCP file should I download?
The Download page auto-detects your operating system, and on macOS whether your chip is Apple Silicon or Intel, then offers the matching build, with the others available under “Other platforms”. The MCP server is available for macOS (Apple Silicon and Intel), Windows, and Linux.
How is MCP different from Agent Mode?
Agent Mode runs inside CellPilot using your own API key. MCP instead lets an outside assistant (Claude Desktop or Codex) call CellPilot's tools. Both let you work in natural language; pick whichever fits your setup.
Troubleshooting
The application won't start
Make sure you are using the correct version for your operating system. On macOS, you may need to right-click the app and select “Open” the first time you launch it. On Windows, you may be prompted to click “Run anyway”.
Analysis is slow
For large datasets, ensure you have sufficient RAM (8GB+ recommended). Closing other applications can help free up memory.
My data format isn't recognized
Check that you selected the correct folder level. For example, scATAC should use a Cell Ranger ATAC-style folder with filtered_peak_bc_matrix, Visium HD should use a Space Ranger output folder or relevant outs/binned_outputs folder, and multiome should use a Cell Ranger ARC output folder. For examples, see the Tutorial page.
Contact & Support
How do I report a bug?
Please open an issue on our GitHub repository.
How can I contribute?
We welcome contributions! Check out our GitHub repository for contribution guidelines.