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
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.
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.