Olympus ScanR

Expected Data Structure

The ScanR converter expects an acquisition directory containing a data subdirectory with the OME-XML metadata file and TIFF images:

my_acquisition/
└── data/
    ├── metadata.ome.xml     # OME-XML metadata file (required)
    ├── image_001.tiff
    ├── image_002.tiff
    ├── ...
    └── image_NNN.tiff

Flexible path input

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

Metadata

The converter parses the OME-XML metadata file using the ome_types library. It extracts:

• Well and position IDs from image names (pattern: W<well_id>P<position_id>)
• Channel names
• Pixel size (physical size X/Y)
• Stage positions per plane (X, Y, Z)
• Z-spacing (computed from plane positions)
• Timepoint information

Well ID Mapping

ScanR uses sequential well IDs (W1, W2, ...) that the converter maps to row/column format based on the plate layout:

Layout	Rows	Columns	Example: W1 = A01, W13 = B01 (96-well)
24-well	4 (A-D)	6	W1 = A01, W7 = B01
48-well	6 (A-F)	8	W1 = A01, W9 = B01
96-well	8 (A-H)	12	W1 = A01, W13 = B01
384-well	16 (A-P)	24	W1 = A01, W25 = B01

Task Parameters

The ScanR init task adds a Layout field to the base acquisition parameters:

Field	Type	Default	Description
Path	str	required	Path to the ScanR 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.
Layout	str	"96-well"	Plate layout. One of: 24-well, 48-well, 96-well, 384-well.
Advanced	AcquisitionOptions	{}	Advanced options (condition table, overrides).

Plate layout

Make sure to set the correct Layout for your plate. The well ID mapping depends on it — using the wrong layout will assign images to incorrect wells.