https://github.com/biop/omero-hrm
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: BIOP
- Language: Python
- Default Branch: main
- Size: 77.1 KB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
OMERO - HRM
These scripts aim at making the connection between OMERO and HRM more friendly. Our HRM server works with a shared folder located on another server (HRM-Share folder). Scripts are uploaded to OMERO.server and can be run from the web interface. Documentation is available on our wiki page
Send image to HRM
The first script sends images from OMERO to HRM-Share folder. You can select image(s), dataset(s) or project(s) IDs and all images are sent to the shared folder,
with the following hierarchy : Raw / omero / projectID_projectName / datasetID_datasetName / Fileset_ID.
Retrieve image from HRM
The second script sends back deconvolved images to OMERO. It uploads .ids images to the same project/dataset as raw images,
adds deconvolution parameters as key-value pairs and attach the .log.txt file as attachment to the image.
Moreover, it adds raw and hrm tags to the raw image, deconvolved and hrm tags to the deconvovled
image and transfer all tags from the raw to the deconvolved image.
An option allows you to clean your HRM folder. If you select Delete deconvolved images on HRM,
only images within the Deconvolved folder of HRM will be deleted.
If you select Delete raw images on HRM, the raw images are also deleted. In both cases, if the
parent folder is empty, it is automatically deleted as well.
Owner
- Name: BioImaging And Optics Platform (BIOP)
- Login: BIOP
- Kind: organization
- Location: Lausanne, Switzerland
- Website: https://biop.epfl.ch
- Repositories: 84
- Profile: https://github.com/BIOP
All the code that is publicly available/published by the BioImaging And Optics Platform (BIOP)