https://github.com/diamondlightsource/python-omexml-dls
Python package for simple and consistent creation and parsing of Open Microscopy Environment (OME) metadata
https://github.com/diamondlightsource/python-omexml-dls
Last synced: 3 months ago
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Python package for simple and consistent creation and parsing of Open Microscopy Environment (OME) metadata
- Host: GitHub
- URL: https://github.com/diamondlightsource/python-omexml-dls
- Owner: DiamondLightSource
- License: other
- Created: 2020-02-10T21:35:04.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2021-09-02T11:26:55.000Z (over 3 years ago)
- Last Synced: 2025-02-17T09:26:46.691Z (3 months ago)
- Language: Python
- Size: 442 KB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# [omexml-dls](https://github.com/DiamondLightSource/python-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](https://github.com/CellProfiler/python-bioformats)' omexml.py with a section from the Allen Institute for Cell Science's [aicsimageio](https://github.com/AllenCellModeling/aicsimageio/tree/master) 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](https://github.com/AllenCellModeling/aicsimageio/tree/master))
* `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