Preparation

# Preparation And Normalization

Operator input files¶

The concrete file-format guidance lives in Preparing input files.

That page documents the runtime contracts for:

• the fluidics program CSV
• the experiment order file
• the codebook CSV

merfish3d_wfacq.ui_state¶

This module contains widget-facing normalization helpers:

• build_merfish_ui_state
• wavelength_rows_for_sequence
• channel_specs_from_sequence_wavelength_rows
• bit_mapping_preview
• fluidics_round_options

These helpers convert the current upstream MDA state and the MERFISH widget state into a normalized Python dict for validation and dispatch.

merfish3d_wfacq.workflow¶

This module validates and normalizes the MERFISH run configuration.

normalize_merfish_ui_state¶

Purpose:

• validate the currently loaded widget state
• enforce the fluidics / experiment-order / codebook contract
• infer the fiducial channel from the unique all-zero experiment order file column
• return one normalized dict for the run

build_merfish_metadata¶

Purpose:

• convert normalized widget state into the metadata used by sequence generation, engine setup, and datastore setup

prepare_merfish_acquisition¶

Purpose:

• add runtime metadata such as resolved experiment root, datastore root, tile count, and z-plane count
• return the prepared event list plus runtime metadata

merfish3d_wfacq.dispatch¶

prepare_merfish_dispatch¶

Purpose:

• create the in-memory drift runtime store when needed
• build prepared events and runtime metadata
• construct the output listener used for run_mda(...)

Returns:

• prepared list[MDAEvent]
• MerfishFrameProcessor | None

This is the narrow non-Qt assembly layer between GUI state and execution.