PerkinElmer Operetta / Opera Phenix

Expected Data Structure

The Operetta converter expects an acquisition directory containing an Images subdirectory with the metadata XML file and TIFF images:

my_acquisition/
└── Images/
    ├── Index.idx.xml        # Metadata file (required)
    ├── r01c01f01p01-ch1sk1fk1fl1.tiff
    ├── r01c01f01p01-ch2sk1fk1fl1.tiff
    ├── ...
    └── rXXcXXfXXpXX-chXskXfkXflX.tiff

Flexible path input

You can point Path to either the base directory (my_acquisition/) or directly to the Images subdirectory (my_acquisition/Images/). The converter handles both.

Metadata

The converter reads all image metadata from Images/Index.idx.xml, including:

• Well position (row and column)
• Field of view index
• Channel names and IDs
• Pixel size (from ImageResolutionX / ImageResolutionY)
• Stage positions (X, Y, Z)
• Z-plane and timepoint indices
• Bit depth (auto-detected from max intensity values)

Task Parameters

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

Field	Type	Default	Description
Path	str	required	Path to the Operetta 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).

Multiple Acquisitions (same plate)

To combine multiple acquisitions (e.g., different timepoints or imaging rounds) into a single plate, use different Acquisition Id values while keeping the same Plate Name.