Install fiji-mcp

beginnergetting-startedsetupfijimcp

by Steffen Plunder

›_ claude — Round 1

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claude — Round 1

% git clone https://github.com/SteffenPL/fiji-mcp.git && cd fiji-mcp

✱ fiji-mcp repository cloned

claude — Round 2

% uv sync

✱ Python environment ready

claude — Round 3

% uv run fiji-mcp install

Fiji found at /Applications/Fiji.app
Bridge plugin copied to Fiji plugins/
Fiji path saved to .fiji-path

✱ bridge plugin installed into Fiji

claude — Round 4

% claude mcp add --scope project fiji-mcp -- uv run --directory /Users/steffen/fiji-mcp fiji-mcp

Added fiji-mcp to project MCP config (.mcp.json)

✱ MCP server registered

claude — Round 5

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Open the ImageJ sample image blobs.gif in Fiji using the run_ij_macro tool with this macro code: open("https://imagej.net/images/blobs.gif");

Fj (Fiji Is Just) ImageJ

"More Tools" menu (switch toolsets or add tools)

Log

[fiji-mcp] Bridge started on port 8765

[fiji-mcp] WebSocket server started on port 8765

[fiji-mcp] Client connected: /[0:0:0:0:0:0:0:1]:502

⚡ fiji-mcp · run_ij_macro

open("https://imagej.net/images/blobs.gif");

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claude — Round 6

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Now get a thumbnail of the opened blobs.gif image using the get_thumbnail tool.

⚡ fiji-mcp · get_thumbnail

title: blobs.gif

Fj blobs.gif 256×254 · 8-bit · inverted LUT

256×254 pixels; 8-bit; inverted LUT

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