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Architecture Overview

LangSlice is organized around one installable Python harness package, langslice_harness, plus a Tauri desktop app and model projects.

Package Layout

  • src/langslice_harness/atlas/ -- BrainGlobe atlas loading, coordinate conversion, and slice extraction.
  • src/langslice_harness/harness/estimation/ -- ADK slice-position estimation agents, prompts, tools, validators, plugins, and runners.
  • src/langslice_harness/harness/estimation/image_gen.py -- image-gen position estimation.
  • src/langslice_harness/registration/ -- public registration wrapper, runtime, solver, and result types.
  • src/langslice_harness/harness/registration/ -- image-gen registration candidate generation and optional ADK review.
  • src/langslice_harness/whole_brain/ -- multi-slice position estimation pipeline.
  • src/langslice_harness/image_prep.py -- image normalization, metadata detection, and downsampling.
  • src/langslice_harness/export.py -- QUINT/ABBA-compatible JSON export.

The CLI command remains langslice, but the Python import package is langslice_harness.

Position Estimation

Single-slice and group position estimation run through ADK. The agent can fetch atlas images and must submit a structured estimate. Native Gemini requests can use the File API for target images, and a persistent multimodal plugin keeps fetched atlas images visible across turns.

Image-gen position estimation is available for visual sweep/zoom style estimation and is used by the whole-brain pipeline.

Image-Gen Registration

Registration has one active method: image-gen registration.

  1. Prepare a histology slice, atlas color map, and atlas reference image.
  2. Ask the image-generation provider to generate an atlas-colored target aligned to the histology.
  3. Register the generated target to the atlas color map with itk-elastix.
  4. Warp the atlas RGB through the recovered transform.
  5. Extract VisuAlign markers from B-spline control points.
  6. Return the generated atlas target, warped atlas, and warped-border overlay.

Direct mode returns the first candidate. Agentic mode lets an ADK review agent inspect up to three candidates before confirming one.

Whole-Brain Estimation

Whole-brain estimation discovers a folder of slices, estimates anchor slices, interpolates positions for non-anchor slices, runs windowed image-gen estimation, and fits a constrained monotonic position curve.

Desktop App

tauri-gui/ contains the Rust backend and React frontend. The GUI invokes the Python harness as a sidecar for position estimation, registration, and export while the Rust side handles atlas loading, reslicing, and mesh serving.

Debugging

Set LANGSLICE_VLM_DEBUG_DIR for run artifacts. Set LANGSLICE_ADK_CAPTURE_REQUESTS_DIR for redacted ADK request captures.