[ome-devel] IDR screen in Zegami

[Roger Noble]

Thanks Douglas, I’ll give that a go and report back ☺

Cheers
Roger

From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Douglas Russell
Sent: Monday, 4 July 2016 4:53 PM
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk>
Subject: Re: [ome-devel] IDR screen in Zegami

I wrote a script for doing something very similar to this:

https://github.com/sorgerlab/OMERO_scripts

It also returns screen_name, plate_name, etc, but you could tweak it to remove that pretty easily.

You will need to clone the repository as there is another python file there which handles OMERO connections and reading user/pass from the config file (as described in the README). Once that's done you should just be able to:

./list_screen_images.py 123 --file output.csv

You could edit the script to remove the csv writing part of it if you want to do something different with the returned data.

Cheers,

Douglas

On Mon, 4 Jul 2016 at 04:05 Roger Noble <roger at zegami.com<mailto:roger at zegami.com>> wrote:
Hi Josh,
Using the code I was able to relatively quickly put together a data set that I could then use to create a Zegami collection.

As you can see I'm iterating over each well and each API endpoint to construct the metadata. I've attempted to do the same for the ' idr0009-simpson-secretion/screenA' screen which is significantly larger and using the current approach will take a very long time to complete.

There is the option to use the annotation.csv file hosted on GitHub but my understanding is that this will still require a secondary set of queries to retrieve the internal OMERO id for each well. If there was a simple way to query an entire screen that contained:

plate well omero_id

that would be very useful.

What do you think?

Thanks
Roger Noble
CTO
http://www.zegami.com



-----Original Message-----
From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk<mailto:ome-devel-bounces at lists.openmicroscopy.org.uk>] On Behalf Of Josh Moore
Sent: Thursday, 23 June 2016 10:48 AM
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-devel] IDR screen in Zegami

On Thu, Jun 23, 2016 at 8:41 AM, Jason Swedlow (Staff) <j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>> wrote:
> Hi Roger-
>
> Thanks so much for this.  A quick look— I’m on not-so-great wifi, but
> seems very nice demo of what we want to enable with the IDR project.
> Please do let update this list when the scripts are available.
>
> Are other comments, suggestions or ideas?

From my side, it'd be interesting to know if you ran into any particular obstacles attempting this. Though I can understand if it's easiest to talk through that once the repo is up.

One minor suggestion is to strip the number from the phenotype keys, treating them all as equivalent since the index carries no information. We're working on performing that cleanup in the source data now.

Cheers,
~Josh.


> Thanks again— this is just great.
>
> Cheers,
>
> Jason
>
>
> From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk<mailto:ome-devel-bounces at lists.openmicroscopy.org.uk>> on
> behalf of Roger Noble <roger at zegami.com<mailto:roger at zegami.com>>
> Reply-To: OME Development <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
> Date: Wednesday, 22 June 2016 23:11
> To: OME Development <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
> Subject: [ome-devel] IDR screen in Zegami
>
> Hi All,
>
> I’ve just put together a Zegami collection based on the
> idr0002-heriche-condensation screen.
>
>
>
> You can have a look at it here http://demo.zegami.com/omero-idr.html
>
>
>
> I’ve also integrated the OMERO viewer to allow access to the time
> points and channels. This can be accessed by clicking an image and
> selecting the “OMERO Viewer” button on the upper right.
>
>
>
> To generate the collection I created a few Python scripts which called
> the JSON api endpoints made available at
> http://idr-demo.openmicroscopy.org. I’m in the process of creating a
> GitHub repository to host the scripts if anyone is interested. I’ll share once it’s ready.
>
>
>
> What do you think?
>
>
>
> Thanks
>
> Roger Noble
>
> CTO
>
> http://www.zegami.com
>
>
>
>
> The University of Dundee is a registered Scottish Charity, No:
> SC015096
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
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