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.