OpenSlide with OMERO.web to render images not renderable by Bio-Formats?

Could you provide a guide on how you installed ome_seadragon? I am trying to use it with the Moodle plugins and I am stuck on where I install it for omero_web app

Hi @Joao_Miguel , I set up ome_seadragon using this Docker compose: https://github.com/fireofearth/ome_seadragon_compose . As of now I’m having some trouble setting up ome_seadragon outside of the Docker compose since it’s only compatible with OMERO.server 5.4.1 and the installation process is pretty convoluted. I may release an updated revision of OME Seadragon to work with 5.5.1 / 5.6 once I get that working.

Sorry if it is a stupid question but what is a Docker? My institutional project depends on me accessing omero to use in moodle so I am extremely interested on installing ome_seadragon. I have installed omero 5.5.1 so I undestand I wont be able to follow your proposal to use ome_seadragon composer. Is that correct? Anything I can help to make it work?

Should I downgrade OMERO to 5.4.1 and try to install it? Could you please give me some guidance on the installation process? I really need to start working with Moodle and this plugin is essential for it

@Joao_Miguel sorry I took awhile to get back to you, Lucas just tried using OME Seadragon on OMERO.server 5.5 and says it works with that version (while I had some trouble with it initially).

see the docker images for testing:
https://github.com/lucalianas/ome_seadragon-docker/tree/ome_5.5
https://github.com/lucalianas/ome_seadragon-nginx-docker/tree/ome_5.5

Since you have are not using Docker you’ll have to install it as a Django plugin directly. You can try using the instructions: https://docs.openmicroscopy.org/omero/5.5.1/developers/Web/CreateApp.html

Unfortunately I can’t help you any more than that right now as I’m also figuring out how to use this outside of Docker.

@fireofearth Docker is a application “container” for running apps in a defined environment with all dependencies etc. Like a light-weight virtual machine. https://www.docker.com/why-docker

Docker compose allows you to set up several Docker containers to compose a complete app. E.g. https://github.com/lucalianas/ome_seadragon_compose/blob/develop/docker-compose.yml has an OMERO database, OMERO server, as well as several of seadragon web containers.
The setup of the ome_seadragon container is in https://github.com/crs4/ome_seadragon-docker/blob/master/Dockerfile, includes install of dependencies such as OpenSlide.

To run https://github.com/crs4/ome_seadragon outside of Docker, you need to have OMERO.web running somewhere. Then you can follow some of those instructions manually.

Essentially, you need to add the folder containing ome_seadragon to your $PYTHONPATH so it can be imported by the OMERO.web framework, and add ome_seadragon to the list of installed apps.

I just tried this (within the Python environment where you’re running OMERO.web)

$ git clone git@github.com:crs4/ome_seadragon.git
$ cd ome_seadragon/
$ pwd
/Users/will/Desktop/SEADRAGON/ome_seadragon
$ export PYTHONPATH=/Users/will/Desktop/SEADRAGON/:PYTHONPATH

Add to omero web apps - NB: note the single-double quotes.

$ omero config append omero.web.apps '"ome_seadragon"'

This was enough for me to restart OMERO.web and go to e.g.

localhost/ome_seadragon/get/projects/
I haven’t tried anything that requires OpenSlide yet…

Will.

1 Like

@Joao_Miguel here’s the updated Docker Compose for OME Seadragon using OMERO.server 5.5. And yes that’s essentially what Docker is and will-more explained it better than I could. For testing you only have to git clone the compose from here https://github.com/fireofearth/ome_seadragon_compose and do docker-compose up inside the repository using your terminal.

Will’s is correct about how to use OME Seadragon outside of Docker, however you also need to set up NGINX and OpenSlide for TIFF/MIRAX. Will get to that later…

Hi Will,
This is the third editing of this post but I thought I should do to facilitate to others:

  1. Cloning ome_seadragon in <your preferred location>:

git clone https://github.com/crs4/ome_seadragon.git

  1. Register the PYTHONPATH
    $ export PYTHONPATH=<your preferred location>:PYTHONPATH

  2. Add to omero web apps - NB: note the single-double quotes.

$ omero config append omero.web.apps ‘“ome_seadragon”’

  1. Check if it works
    http:/localhost/ome_seadragon/get/projects/

I struggled a bit with the cloning, PYTHONPATH as well as appending twice ome_seadragon, so I thought to put in a different format (your explanation was correct, but i struggled to understand it at first).
Many thanks

It might be a silly question to linux geeks but I am struggling to find a solution. I managed to add PYTHONPATH onto my .bash_profile so seadragon is found without problems but only if I login and run omero.web. A simple reboot does not start it. Is there a way to sort this out?

That will likely depend on how OMERO.web is getting restarted on reboot. Are you using a System-D script? A cron job? ~J

Systemd. I am actualy looking at the omero-web-systemd.service file. Shoud I add

export PATH
export PYTHONPATH=(the python folder)

there instead of on ~/.bash_profile?

Likely both, but for the automatic restart, your .bash_profile will be ignored.

1 Like

I added the following to /etc/systemd/system/omero-web-systemd.service
before the ExecStart command:
Environment=“PYTHONPATH=<path to app/>:PYTHONPATH”
and now it is working at any reboot

1 Like

I managed to install ome_seadragon as well as the omero-repository on moodle.
However, I have no clear information on how to setup them. Most complicated for testing is how to to get the OmeSeadragon API key and API secret. There is a comment about using OMERO API Endpoint>/apps but I have no idea on how to find this.
Any suggestions?

Hi @Joao_Miguel

I just finished creating the install script for my lab. It’s not done yet and I will have to update it again later today. However this should more or less gets Postgres, NGINX, Redis, Node.js+NPM, OMERO.server, OMERO.web, OME Seadragon (everything! except for moodle stuff) installed on a new machine in one command:

bash setup.sh  --pip --npm --upgrade

This script also doubles as a step by step guide to setting everything up if you can read BASH. Note this only works with Ubuntu 18.04 with systemd. It also creates a startup systemd startup script that runs OMERO.server and OMERO.web on system startup.

After running the script, go to http://localhost/ome_seadragon/test/ to check that it works. You can also view images that you uploaded by going to http://localhost/ome_seadragon/example/viewer/<Image ID>/

1 Like

This is a great work @fireofearth, many thanks. I had it installed on a centos machine but I will keep in mind for reference. The link http://localhost/ome_seadragon/test/ works for me.I assume I can use your commands to create the ome_seadragon public user.
However, I am still stuck on where to find the OmeSeadragon API key and API secret, both required for the connection to Moodle. If you can shed any light on that subject I would appreciate.
Thanks

Unfortunately I have no experience running Moodle, so I’m not able to help you. Since this thread is not about Moodle I encourage you to create a post about Moodle and OMERO integration.

Alternatively, you can get in touch with the creator of OME Seadragon. He’s quite open to helping others with it.

Dear all, sorry if I was able to get in touch with you only now. I’m Luca Lianas, I work at CRS4 (Center for Advanced Studies, Research and Development in Sardinia) and I’m the developer of the ome_seadragon plugin for OMERO.web.
I’ve been in touch by email with some of the users that are using the software.
Since I’m not an “regular” visitor of this forum, I’d like to suggest to move all the questions related to ome_seadragon to the GitHub repostitory of the project (https://github.com/crs4/ome_seadragon). In there you can compile issues related to software installation or its functioning and I’ll be able to interact with you swiftly, also we’ll be able to create some kind Q&A section.
I also wanted you to know that at the following link https://github.com/lucalianas/ome_seadragon_compose you can find the docker-compose file with the full stack needed by ome_seadragon to work. You can use this as base to install the software by using Docker or to know how it can be configured.
I hope this message was usefull. See you on GitHub!

2 Likes

@fireofearth
Hi, my Name is Simon and im also in the process of getting to know the workflows and routines around high resolution image storage/processing.

You mention:
Note Mirax requires an importer and not just omero import
May i this Question:
I got docker up and running and also am able to import images into Omero via the standart CLI and insight as well. The Crux no is how did you get your mirax files visible in web. Using the mentioned import skript i was able to sucessfully execute it inside the Docker container on the directory the images are stored in (file.mrxs file) and it recognizes the files. After that step the files dont seem to show up in OME_web.

So how do you actually get WEB to initialize the viewer on the images ?