greenpolo/langslice/abba

ABBA from a coding agent

For the main session. A job started from ABBA (the user chose Register › LangSlice… in ABBA) is an ordinary LangSlice job in ~/.langslice/abba/<project>/ whose images are ABBA's snapshots: the user pastes the LangSlice window's message, and langslice-job FOLDER init continues the prepared job (ABBA's positions, cutting angles, pixel size and protected registrations are already in it; do not pass them again). While ABBA is open, every write to that job appears in ABBA as one ABBA Undo step; nothing else is needed to "send results to ABBA". Registration itself is the subagent's work (register-brain skill).

Reaching a running ABBA: abba-mcp

abba-mcp is ABBA's MCP server, released with ABBA 0.25.0 (installation: https://abba-documentation.readthedocs.io/en/stable/installation/installation.html#install-assistant). It needs uv. Register uvx abba-mcp as a local (stdio) MCP server:

codex mcp add abba -- uvx abba-mcp
# Fiji without a window:
codex mcp add abba --env ABBA_MCP_HEADLESS=true -- uvx abba-mcp

In another client: server abba, command uvx, argument abba-mcp.

• The first Fiji tool call downloads Java, Fiji and ABBA into ~/.abba-mcp,

which takes minutes: tell the user, and call the tool again. That Fiji is abba-mcp's own; it does not use or change the user's Fiji.

• If a Fiji already answers on port 9090 running ABBA 0.25.0 (the user's own

Fiji, its MCP server started from Help › Assistants › Manage Fiji MCP Server…), abba-mcp drives that one instead. A Fiji there running another ABBA version is refused, with a message to close it.

• Only the user's own Fiji has the LangSlice connector installed (ABBA's

Register › LangSlice…); the Fiji abba-mcp downloads does not.

• Before the first command, read abba-mcp's guide with abba_docs_read

(guides/abba.md: the workflow and its traps; abba_docs_search searches its docs). Commands run by title with fiji_module_run; fiji_module_describe gives a command's inputs, defaults and choices. ABBA's documentation for this version: https://abba-documentation.readthedocs.io/en/v0.25.0/

Never give these tools to a registration subagent. Without the server, ABBA is driven by the user: give them the exact menu steps.

ABBA 0.25.x commands (menu path under Plugins > BIOP > Atlas)

Start a session first (Open Atlas, then ABBA - ABBA Start; without a window, ABBA - Align Big Brains and Atlases (no GUI)); every command below acts on that ABBA session.

Names and parameters were read from the ABBA source at tag ImageToAtlasRegister-0.25.0; other ABBA versions may differ.

With a LangSlice job that did not start from ABBA

• Into LangSlice: export from ABBA (QuickNII dataset, or the registration

file) and start the job from it: langslice-job FOLDER init --registration FILE.

• Out of LangSlice: there is no correct way to put such a job's results into

ABBA. Never import its quicknii.json with ABBA - Import QuickNII Project: ABBA reads the JSON's width and height (the original image's) as the size of the PNG copy, so large images shrink toward a corner, and it takes one median cutting angle along each image's own axes, so the sections land millimetres off and out of order. To use ABBA, start the job from ABBA. For other programs, see step 5 of the register-brain skill.

• ABBA's coordinates differ from BrainGlobe's by a measured offset of about

0.985 mm. Never hardcode it or convert positions by hand.

• Save State before any bulk change.