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OME-TIFF

OME-TIFF Specification

We aim to fully comply with the official specification for OME-TIFF as defined by:

https://ome-model.readthedocs.io/en/stable/ome-tiff/index.html

ome-writers supports writing to OME-TIFF, a stable and widely used standard for storing multi-dimensional biological image data. OME-TIFF is an extension of the standard TIFF format that includes metadata defined by the OME-XML Data Model to describe the higher order dimensionality and experimental context of the image data.

Expected Output Structure

When writing an acquisition to OME-TIFF, the expected output structure depends on your AcquisitionSettings. OME-TIFF supports no more than 5 dimensions per image (strictly: T, C, Z, Y, X). Therefore, acquisitions with additional dimensions (e.g., stage position, tiles, angles, etc.) are broken into series of ≤5D images. The OME-TIFF specification supports arranging those series either in a single large file, or as multiple files in a directory structure. ome-writers currently only supports the latter approach: positions/series are always written as separate files in the output directory

Any acquisition with a combination of no more than "TCZXY" dimensions is stored as a single OME-TIFF file, directly at the AcquisitionSettings.output_path.

Example Code

Writing a single ≤5D image

Acquisitions that contain multiple positions (e.g., stage positions, tiled images, angles on a light-sheet microscope, etc.) or that exceed 5 dimensions in any way other will be structured as multiple OME-TIFF files, one per position/series. For example, if AcquisitionSettings.root_path is "dest/my_file.ome.tiff" and there are 4 positions in a position dimension (type='position'), the output will be:

dest/my_file_position_p000.ome.tiff
dest/my_file_position_p001.ome.tiff
dest/my_file_position_p002.ome.tiff
dest/my_file_position_p003.ome.tiff

Example Code

Writing multiple positions

If you declare AcquisitionSettings.plate along with a position dimension (type='position') containing Positions that define plate_well/plate_column information, the output follows the same pattern as above, but HCS metadata is included in the OME-XML. Work in progress: full support for HCS metadata in OME-TIFF is still being developed.

Example Code

Writing plates

Backends

  • tifffile (default): Uses the popular tifffile Python library to write OME-TIFF files, and ome-types to generate the OME-XML metadata embedded in the TIFF header.