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Pipeline Database Integration
Edward O'Donnell edited this page Feb 26, 2020
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- Done in new pipeline
- All operations are logged in a database table.
- CZI file to TIF - done on muralis, approx 6 minutes per czi file.
- Slides table gets updated with status, time and file size of each czi file
- Slides_czi_to_tif table gets updated with status, time and file size of each tif file
- Set depth to 8 for all images.
- Flip, rotate all images.
- Linear normalize for counter stain channel, normalize other channels according to new algorithm.
- Adaptive normalization.
- Channels combined into one image for sections.
- Scaled down images set available for viewing.
- Done in existing GUI that has been upgraded to Python 3.
- All necessary GUI files and supporting files imported in the new pipeline project.
- All files cleaned up of any unnecessary code and ported to Python 3.
- All files run through pylint
- Files renamed to proper numbering.
- Precomputing step for Neuroglancer
- Precomputed files placed in appropriate dir for access by web server.