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Quickstart

# Quickstart

This quickstart assumes you already have a working Micro-Manager configuration and a Python environment with merfish3d-wfacq installed.

Launch the application

merfish3d-wfacq --mm-config C:\path\to\MMConfig.cfg

You can also start it without a config and load hardware later:

merfish3d-wfacq

Configure the upstream MDA widget

Before using the MERFISH dock:

  • choose the active channel group and channel configs
  • configure stage positions or Stage Explorer tiles
  • configure the z plan
  • choose the save destination in the MDA widget
  • keep the MDA configuration consistent with the MERFISH files you plan to load

Prepare the MERFISH files

Before loading files into the MERFISH widget, prepare:

  • a fluidics CSV when the selected mode uses fluidics
  • an experiment order file for imaging runs
  • a codebook for imaging runs
  • measured illumination profiles, or plan to enable Use uniform / unknown illumination

Use Preparing input files for the exact file formats and validation rules.

Load MERFISH inputs

In the MERFISH widget:

  • choose a run mode
  • load the fluidics CSV when the mode uses fluidics
  • load an experiment order file for imaging runs
  • load the codebook for imaging runs
  • load illumination profiles, or enable Use uniform / unknown illumination

Check the contracts

Before running:

  • the experiment order file must contain one column per active channel config name
  • experiment order file column order does not matter
  • exactly one experiment order file channel column must be 0 for every round, and that column is the fiducial channel
  • fluidics-only runs do not require any RUN step; they execute all rounds in the fluidics program
  • iterative imaging requires at least one RUN step in the fluidics program
  • iterative imaging requires experiment order file rounds to match the fluidics rounds that contain RUN
  • the codebook must contain enough bit columns for the highest bit used in the experiment order file
  • measured illumination profiles must match the number of active channels

Run the acquisition

  • use Run fluidics for fluidics-only programs, including programs with no RUN rows
  • use Run acquisition for full iterative MERFISH imaging
  • use Run single round imaging for a one-round test
  • use Abort to cancel a running acquisition

Handle REFRESH steps

If the fluidics program includes REFRESH:

  • perform the manual operator step
  • click Yes in the dialog to continue
  • click No to stop advancing the run

Validate output

Imaging runs create a qi2lab datastore under the resolved experiment root:

<experiment-root>/qi2labdatastore

The image arrays are streamed through ome-writers, and the resulting datastore can be validated with the qi2lab analysis stack.