The MCP server link is unstable.

[huiwang266]

• I successfully loaded the file once and confirmed spatial coordinates exist:

• Dataset: card_spatial
• Shape: 428 cells × 25,753 genes
• Spatial coordinates: available

Then the ChatSpatial backend connection dropped (Transport closed) during tissue-structure analysis/plotting, and all
subsequent tool calls failed, so I couldn’t render the tissue structure figure in this session.

1. Restart the ChatSpatial MCP server/session.
2. Tell me to retry, and I’ll run:
   • identify_spatial_domains (or spatial clustering fallback)
   • visualize_data to output the tissue-structure plot immediately.

[cafferychen777]

Hi @huiwang266, thanks for reporting this!

We identified the root cause: external ML libraries (STAGATE, GraphST, SpaGCN, BANKSY) were printing debug/progress text to stdout, which corrupted the MCP JSON-RPC stream and caused the "Transport closed" error.

Fix (released in v1.1.7): All library calls in spatial_domains.py are now wrapped with suppress_output() to redirect their print() output away from the MCP communication channel. This is the same approach already used successfully in other tools (velocity, trajectory, etc.).

To update:

pip install --upgrade chatspatial

Could you try running identify_spatial_domains again with v1.1.7 and let us know if the connection stays stable? Thanks!

[huiwang266]

Thanks! I'm running successfully now.