An ImageJ plugin to run a script on a batch of images from/to OMERO.
Once installed, the plugin is accessible from "Plugins > OMERO > Batch process...".
Specify if you want to process images from OMERO or from a local folder. If you choose "OMERO", a connection window will appear.
If you want to process images from OMERO, once connected, select the dataset you want to process in the "input" panel. You may have to change the group, user or project to get to the required dataset. You can also specify if you want to load ROIs from the images or if these should be removed before saving the results (useful if you want to replace ROIs).
If you chose to process local images, you have to browse and select a folder in the "input" panel. To treat subdirectories, you have to check the "recursive" option.
In the "macro" panel, you have to browse and set the script file that will be used to process each image. If you use the plugin in ImageJ2/Fiji, you should be able to choose a script in any supported language. You can then set the arguments for this script:
getArguments()
though).You also have to specify which output is expected for this script: new image(s), tables, ROIs and/or logs.
Finally, you have to specify if the results have to be saved locally, on OMERO or both. Furthermore, if you save new images, you can set a suffix to append to the images names.
You only have to set the output folder.
You have to select a project you own, or a dataset if you want to save new images. Be aware of the following:
As OMERO handles 3D ROIs, it is possible to store these. However, the script used should generate ROIs and add a "ROI" property to each, and set the same numeric value for those who belong to the same 3D object.
Conversely, if ROIs are loaded from OMERO, they will have two properties set, "ROI" and "ROI_ID":