Writing And Datastore Setup¶

merfish3d_wfacq.datastore¶

prepare_qi2lab_datastore¶

Purpose:

• create the qi2lab datastore layout at sequenceStarted()
• write static datastore metadata and target sidecars
• create shading-map outputs through ome-writers

This module is setup-only. It does not stream acquisition frames.

merfish3d_wfacq.sink.MerfishFrameProcessor¶

Purpose:

• receive frameReady(img, event, meta) from pymmcore-plus
• apply camera offset, gain, and illumination correction
• capture the round-1 fiducial drift reference stack in memory
• forward corrected frames to the datastore writer

merfish3d_wfacq.sink.Qi2labDatastoreWriter¶

Purpose:

• prepare the datastore at sequenceStarted()
• route frames using metadata already stamped onto prepared image events
• build standard frame metadata from the upstream payload
• append arrays using ome-writers
• close per-target streams after the final frame for that target

Upstream contracts reused¶

• CMMCorePlus.run_mda(...)
• sequenceStarted / frameReady / sequenceFinished
• pymmcore_plus.mda._sink._frame_meta_to_ome(...)
• ome_writers.create_stream(...).append(...)

Stage-position contract¶

The writer uses only the runner-delivered payload metadata for position:

• no MMCore position queries in the writer
• no planned-position fallback in the writer
• actual stage coordinates are taken from meta["position"]