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Yokogawa CQ3K

Expected Data Structure

The CQ3K converter expects an acquisition directory containing the measurement metadata files and TIFF images:

my_acquisition/
├── MeasurementData.mlf      # Image measurement records (required)
├── MeasurementDetail.mrf    # Acquisition details and channel info (required)
└── <subdirectories>/
    ├── image_001.tif
    ├── image_002.tif
    ├── ...
    └── image_NNN.tif

The TIFF file paths are referenced inside MeasurementData.mlf and can be in subdirectories relative to the acquisition directory.

Metadata

The converter parses two XML files:

  • MeasurementData.mlf — Contains one record per acquired image tile, including well position (row, column), field index, channel, Z-index, timepoint, stage coordinates (X, Y, Z), and the relative path to the TIFF file.
  • MeasurementDetail.mrf — Contains acquisition-level metadata: pixel dimensions, number of channels, rows/columns/fields/Z-planes/timepoints, and channel details (pixel size, bit depth).

Z-Image Processing

Some CQ3K acquisitions produce multiple image types per Z-stack (e.g., focus, maximum_projection). The converter groups these into separate plates automatically, using the z_image_processing value as a suffix on the plate name.

For example, an acquisition named MyPlate with two Z-processing types will produce:

  • MyPlate_focus.zarr
  • MyPlate_maximum_projection.zarr

If no Z-image processing is present, a single plate is created without any suffix.

Task Parameters

The CQ3K init task uses the base acquisition parameters with no additional fields:

Field Type Default Description
Path str required Path to the CQ3K acquisition directory.
Plate Name str or null null Custom plate name. Defaults to the directory name.
Acquisition Id int 0 Acquisition identifier for multi-acquisition plates.
Advanced AcquisitionOptions {} Advanced options (condition table, overrides).