Yokogawa CellVoyager

Expected Data Structure

The CellVoyager converter expects an acquisition directory containing the measurement metadata files and image files:

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

The image file paths are referenced inside MeasurementData.mlf (with .tif extension) and can be in subdirectories relative to the acquisition directory. The actual files may use .png or .tif extension — select the matching extension via the image_extension parameter.

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 image 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

Unlike the CQ3K converter, the CellVoyager converter does not support Z-image processing types (e.g., focus, maximum_projection). A single plate is always produced per acquisition.

Task Parameters

The CellVoyager init task extends the base acquisition parameters with one additional field:

Field	Type	Default	Description
`Path`	`str`	required	Path to the CellVoyager 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.
`Image Extension`	`"png"` or `"tif"`	`"png"`	File extension of the actual image files. The metadata always references `.tif`, but actual files may be `.png` or `.tif`.
`Advanced`	`AcquisitionOptions`	`{}`	Advanced options (condition table, overrides).

Limited Testing

This converter has been tested on a limited set of acquisitions. It may not work correctly on all Yokogawa CellVoyager datasets.

Python API

from fractal_uzh_converters import convert_cellvoyager, CellVoyagerAcquisitionModel

acquisitions = [
    CellVoyagerAcquisitionModel(
        path="/path/to/cellvoyager/acquisition",
        plate_name="my_plate",
        acquisition_id=0,
        image_extension=".tif",
    )
]

convert_cellvoyager(
    zarr_dir="/output/zarr",
    acquisitions=acquisitions,
)

See How to Run the Converters for all common parameters and execution details.