cellmap_flow.ai_annotate
========================

.. py:module:: cellmap_flow.ai_annotate

.. autoapi-nested-parse::

   AI-assisted annotation: a hosted model proposes a mask for one plane, the user reviews it.

   In the Finetune tab the user points at a structure and asks for it to be
   annotated; the dashboard sends that plane of raw EM to a model with a prompt
   asking it to paint the structure, turns the reply into a mask, and stages it
   for the user to accept into the annotation volume or reject.

   - ``config``: the server-side config that turns the feature on and lists
     the providers and models it may use. Off without it.
   - ``errors``: ``AIAnnotateError``, a category and a message safe to show.
   - ``secrets``: redacting secrets from logs, and reading API keys safely.
   - ``usage``: the per-user daily call limit.
   - ``images``: checking a model's image before decoding it; PNGs for the browser.
   - ``organelles``, ``prompts``: what the model is told about each structure.
   - ``mask_extraction``: EM plane to RGB, and the model's reply to a mask.
   - ``backends``: the providers (Vertex Gemini, a local fake) behind one interface.
   - ``geometry``, ``pipeline``, ``staging``, ``audit``: which plane to read and
     where its mask goes, staging the result for review, and the audit log.

   Import the submodule you need; this package imports none of them, so the
   SDKs a provider needs load only when a call is made.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/cellmap_flow/ai_annotate/audit/index
   /autoapi/cellmap_flow/ai_annotate/backends/index
   /autoapi/cellmap_flow/ai_annotate/config/index
   /autoapi/cellmap_flow/ai_annotate/errors/index
   /autoapi/cellmap_flow/ai_annotate/geometry/index
   /autoapi/cellmap_flow/ai_annotate/images/index
   /autoapi/cellmap_flow/ai_annotate/mask_extraction/index
   /autoapi/cellmap_flow/ai_annotate/organelles/index
   /autoapi/cellmap_flow/ai_annotate/pipeline/index
   /autoapi/cellmap_flow/ai_annotate/prompts/index
   /autoapi/cellmap_flow/ai_annotate/secrets/index
   /autoapi/cellmap_flow/ai_annotate/staging/index
   /autoapi/cellmap_flow/ai_annotate/usage/index