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lucalianas / ome_seadragon_compose

Docker compose to run a system based on ome_seadragon + ome_seadragon_gateway
MIT License
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*.mrxs file import #1

Open S-Streit opened 4 years ago

S-Streit commented 4 years ago

Hello,

The issue is not really a bug just me not figuring out your workflow. How is the .mrx import towards Omero supposed to be conducted. I know there is a Importer Python Script importer for the given job. The Mirax Importer lies within the tools in the modified web container itself. How is the import process supposed to be conducted such that a given .mrxs file is visible in Omero Web afterwards (within the Docker GW structure i can import but web shows nothing afterwards). Or am i getting something wrong.

The Docker consists of Nginx Webserver and Server etc.; Please let me know if there is standart workflow/method this is supposed to work; i.e.:

Which Docker Structure --- > Gateway or just direct Nginx; How and where to call the *.mrxs Import script in order to be able to create ome_objects that can then be opened.

Again this is very close to the "standart" Omero Workflow, so maybe i am completely on the wrong lead here.

Greetings Simon

lucalianas commented 4 years ago

Hi, *.mrxs files can't be handled directly by OMERO but are supported by ome_seadragon thanks to openslide; to make it possible for ome_seadragon to interact with OMERO to store and retrieve these kind of images, I used the OriginalFile objects provided by OMERO (basically it's the way OMERO uses to store non-image files within its database such as scripts or HDF5 tables).

ome_seadragon has a dedicated importer in the tools directory called mirax_importer.py , it collects all the *.mrxs files (and related data folders) located into a folder that must be specified as input parameter to the script.

To make it work with the docker-compose, you must define a volume or mount an existing local folder in both omero-server and ome_seadragon-web with the same path and run the importer script from the ome_seadragon-web container. All the *.mrxs files with a related data folder (file and folder must have the same name) will be imported in OMERO as OriginalFile objects and will be accessible through ome_seadragon's API using the URLs starting by mirax (the ones starting at line 89 of urls.py https://github.com/crs4/ome_seadragon/blob/develop/urls.py#L89).

Best regards, Luca

S-Streit commented 4 years ago

Thank you :) yeah i was just discovering those files yesterday :). Thank you for the explanation and where to run the importer :)