/python-omexml-dls

Python package for simple and consistent creation and parsing of Open Microscopy Environment (OME) metadata

Primary LanguagePythonOtherNOASSERTION

omexml-dls

Package to help simply and consistently create and parse OME metadata for B24 of Diamond Light Source Ltd. This is a modified copy of python_bioformats' omexml.py with a section from the Allen Institute for Cell Science's aicsimageio version of omexml.py (indicated within the file). This package extends capabilities, predominantly in terms of ROIs, while offering a light-weight distribution of the omexml file.

Recommended import:

from oxdls import OMEXML

Current changes (compared to python-bioformats)

  • TiffData - this allows IFDs to be defined (created using set_tiffdata_count(value)) (from aicsimageio)
  • set_ and get_ExposureTime() functions have been added
  • X, Y, Z units have been added for each plane
  • Square ROIs (an roiref must be created for each ROI first, then ROIs are created using set_roi_count(value), then for each ROI: ROI > Union > Rectangle, where ROI parameters can be set)
  • Small formatting changes to improve consistency