version: "1.0.1" name: register-brain description: Set up and run a LangSlice registration of one brain (a folder of histology section images to a BrainGlobe atlas): create the job with the user's choices, hand it to a registration subagent, then check and export the results. Use when the user asks to register, align or place brain sections in an atlas.

Register a brain with LangSlice

You (the main session) prepare the job, launch a registration subagent, check what it produced, and handle import and export with other software. You never do the registration yourself: no positions, transforms or fits written by you. Registration is always the subagent's, and it registers exactly one brain.

1. Ask the user (only what is not already said)

• The folder of section images.
• Tasks: Positioning (order and position along the atlas), Linear (in-plane

alignment), Nonlinear (a deformation per section). Default is positioning plus linear.

• Atlas (default allen_mouse_25um) and cutting plane (coronal, sagittal,

horizontal).

• Nonlinear only: an image model (openai-oauth, openai-api, gemini-api)

or none (--image-provider none, fits to the stain alone).

• Section pixel size in um if the files do not carry it (--pixel-size-um),

and section thickness and interval (--thickness, --interval).

• An existing registration to start from (QuickNII or VisuAlign JSON/XML,

DeepSlice CSV/JSON/XML, or a LangSlice registration.json): --registration FILE. With it and no --tasks, the placement is kept and only the nonlinear step runs.

• Notes about the brain (a tear, a damaged section).
• Which subagent the user allows (step 3).

init takes the job flags langslice-job schema init lists (each with its help, default and choices), among them --notes TEXT (the user's notes, saved in the job). Check that langslice-job runs (langslice-job ops); if it does not, tell the user how the plugin README says to install it, and stop.

2. Create the job

langslice-job FOLDER init --tasks position,transform --atlas allen_mouse_25um \
  --pixel-size-um 4.0 --image-provider none

It prints one JSON object (ok, result, artifacts with the job's card and state, warnings). Report any warning to the user (for example what a --registration file did not place). A job already in the folder is continued; changed inputs are refused with INPUTS_CHANGED and other job settings with SETTINGS_CHANGED, which both name --fresh: ask the user before starting over.

3. Launch exactly one registration subagent

Pick the variant the user allows:

Ask Codex to spawn that custom agent by name. The request names only the job folder: "Register the brain in job folder FOLDER". Add the user's notes only if they were not already saved in the job. Do not add registration advice of your own: the subagent works from LangSlice's own job statement and card. Do not give it any other task. Run one subagent per job at a time.

Shell restriction: Codex rules govern commands that run outside the sandbox only. If the user wants the agent limited, point them to connectors/codex/README.md (rules file and sandbox) before launching.

4. Check the result yourself

When the subagent returns, do not trust its summary alone:

• langslice-job FOLDER status: the job's state, tasks and open items;

confirm the job was submitted.

• Open FOLDER/registration.json (derived from state.json, the truth) and

the exports under FOLDER/exports/ (quicknii.json, visualign.json). Submit writes no per-section maps: langslice-job FOLDER export_maps writes them when they are wanted. docs/file_formats.md in the LangSlice repository describes every file.

• Look at the pictures the job saved (views/, paths in artifacts) by

opening them, and tell the user in plain words what looks right and what does not. If a picture and a number disagree, say so.

• Changes the user asks for go through another subagent run on the same job

(every write is one undo step), not through your own edits.

5. Import and export with other software

langslice-job FOLDER export_maps writes each placed section's maps, exports/quicknii.json, exports/visualign.json and registration.json from the job as it stands. Starting from another program's registration is init --registration FILE (step 1). For ABBA, Fiji, QuPath or QuickNII, use the abba skill.