[ome-users] Question about image analysis and annotations in OMERO

Wed Nov 26 17:28:18 GMT 2014

Hi Christophe

Regarding annotations, attaching files like csv to images is certainly something people do often by creating file
annotations on the server and linking them to existing objects like images.
The full list of structured annotations is available at:
http://www.openmicroscopy.org/site/support/omero5/developers/Modules/StructuredAnnotations.html
The choice for a type of annotation is really dependent on the context and the nature of the data that needs to be
stored back onto the server.

There are also some types of data which can be stored under other forms than an annotation. Masks (and more
generally ROIs) are an example as described by Michael and Ian. Tabular data is another example.

About large-scale analysis, running analysis on a desktop client using the OMERO API works to a certain extent. But
you are right that this approach does not scale with high-throughput or very large data or simply when running
computationally intensive analysis.

For client-side analysis, to some extent, the in-place import solution which has been implemented since 5.0.0 brings
new generic ways to address this challenge. On the one hand, images can be imported and stored into OMERO and
you can use the API for database operations. On the other hand, the original files remain on the filesystem and can be
accessed from an HPC cluster for processing.

Best,
Sebastien

On 26 Nov 2014, at 15:18, Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>> wrote:

Hi Cristophe

Further to this, I’ve just been working on saving binary mask ROIs into images on OMERO from FLIMfit - another Matlab tool.
This code is on Github if you want to take a look.

Ian

On 26 Nov 2014, at 15:10, Michael Porter <m.porter at dundee.ac.uk<mailto:m.porter at dundee.ac.uk>> wrote:

Hi Christophe

There indeed are workflows that take image data and metadata from an OMERO server and do some processing before saving back to the server. And we have instances where OMERO acts as the link between analysts, microbiologists and mathematicians, so definitely not just a data dump! I can't start to answer all of your questions, but in writing tools for semi-automated image analysis I've had to address some of your queries already.

The OMERO.mtools application has workflows to perform various tasks which result in different types of output, from tabular numerical data to mask images and ROIs. Numerical data is saved as .xls on Windows and .csv on Mac to the user's local disk which they can then attach to projects, datasets etc. as they see fit. Automating this attachment step was decided against in this instance as different users expected data to be attached to different things by default. mtools aims to have generic workflows, but if you had a more specific workflow in mind then automated attachment would be very easy. Also, and I might be wrong about this, but I don't think there's a limit to the types of files that can be attached. If the attachment contains text then it will be indexed by the server. This gives another route for finding images by searching for results.

When it comes to segmentation masks, mtools saves a new binary image into the same dataset as the original image. This was written before the introduction of masks as layers of an image. This can be used in Matlab scripts and applications from the createMasks function in the OMERO Matlab toolkit.

mtools doesn't do anything that is considered high-throughput, though it is aimed at batch processing of datasets. In my experience of handling screening data to be analysed in Matlab, I was so happy when I started using OMERO to handle the images!! I wasn't using a cluster to do the crunching on, and I found that as datasets grew the filesystem just couldn't handle it (>15000 images in a directory). And then I was working from a network file server.... It was fairly awful. No doubt FSs have moved on since I last did that work in 2008, so I might be naïve, but I would still rather navigate a screen by calling information from a db than asking an OS to do that level of file management.

Sorry if this is rambling a bit, I hope it helps you. Happy to discuss further if you'd like to.

Regards,

Michael.

-----Original Message-----
From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Christophe TREFOIS
Sent: 26 November 2014 12:27
To: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: [ome-users] Question about image analysis and annotations in OMERO

Dear all,

Do you know of any workflows where people use OMERO, analyse images outside of OMERO and then attach the results back to the original image.

I know this is the basic premise of OMERO, however I am wondering if somebody has some experience with specific applications, such as:

1. Do people typically attach a .csv file to the original image?
2. Which kind of annotation to the image itself is possible and useful?
3. How do people interact with the annotated items?
- Do they download the .csv and look at it in Excel?
- Can they see segmented cells in their OMERO web?
- If yes, where do they see the segmentation? On the same image, on a separate image?

I would be really interested in discussing with some people who have already dealt with this and especially with automated image analysis. For instance, we will have several people doing only image analysis and other people acquiring the images. Obviously, OMERO could be the bridge between these groups of people, but we want to use OMERO for more than just a database to dump your data.

Also, does anybody have any experience on launching scripts from OMERO on an High performance cluster?

And finally, for high-throughput cases, what is some workflows that people use? Currently, it seems much faster to just load the images from the filesystem, rather than using the OMERO API which slows down transfer of images and opening them dramatically.

Any pointers, discussion, documentation, will be extremely welcomed!

Thank you for your help in this,

—
Christophe
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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

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