Open Microscopy Environment

I was trying to read in SVS files generated by an Aperio Microscope directly into OMERO---- the bioformats library says it supports the SVS format itself, but when I Tried to actually select the image it was not one of the options. I was trying to do this through the GUI importer module using the 4.0.3 server install.

Any help would be appreciated-- plan B I guess would be trying to use the native bioformats library and perhaps translating the SVS file to a different format that OMERO could then read directly-- I am just trying to simplify my life as much as possible!

Thanks

DG

Hi DG,

I sent you a response via the feedback mechanism before I saw this message, so I'll just quickly reiterate here.

Basically importer doesn't support everything that's in bio-formats just yet. This is because bio-formats and OMERO handle the extended meta data differently. We are currently working to 'unifiy' these differences, but until then, OMERO only supports some 30 odd formats from the larger list in bio-formats.

To see which formats are currently supported in OMERO, you can check out this link:

http://trac.openmicroscopy.org.uk/omero ... terFormats

In order to import tiff images which are not currently supported, you will have to convert them into a different format which is supported, such as ome.tiff. ImageJ should provide you with the means to access your images through bio-formats and re-save them.

Cheers,

Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee

I have a related question. I have some files in the Aperio svs format and want to access them over the web. Currently, I download them from my server and use Aperio's ImageScope software on the client side to view them. Of course, the download can be a slow process for large files. I was hoping that Aperio would provide their web server (ImageServer), but they apparently don't sell that separately. I guess that's because they want you to buy their $74,000 Spectrum software that includes ImageServer.

In any case, I am looking for a web server that will allow me to view svs files over the web, without downloading them. What, if any, product should I use in the OME software suite? It sounds like svs files are not currently supported, but that you have a work around in mind. Please elaborate on any file conversions required and the exact software I should use. Is the OME platform able to image with Aperio's ImageScope, or would you suggest a different client application? I would very much appreciate your guidance on the use of svs files and, in general, the viewing of large image files of other formats over the web with OME. Thanks.

sac wrote: I am looking for a web server that will allow me to view svs files over the web, without downloading them. What, if any, product should I use in the OME software suite? It sounds like svs files are not currently supported, but that you have a work around in mind. Please elaborate on any file conversions required and the exact software I should use. Is the OME platform able to image with Aperio's ImageScope, or would you suggest a different client application? I would very much appreciate your guidance on the use of svs files and, in general, the viewing of large image files of other formats over the web with OME. Thanks.

Hi Sac,

The OMERO.web application will let you view images with a web-browser once they are stored in an OMERO.server, but to really answer your question we'll need a bit more information. Can you elaborate on what exactly you're trying to do? For example, how large are the images you're working with and what sort of work flow are you trying to create?

Also, we are planning on turning on a number of new file formats for the next release and (depending on the success of our testing) SVS may be among them. If you're comfortable experimenting however, you can also go into the importer's config folder and enable the svs file format in the 'importer_readers.txt' file and try it yourself.

Hope that helps,

Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee
(The University of Dundee is a registered Scottish charity, No: SC015096)

Hi Brian:

Thanks for your reply. We have an application that includes a repository of multimedia information. We'd like to find a way to view standard format images on the Web in the same way that we view videos using servers such as Windows Media Server and RealPlayer. The OME web server seemed like a logical choice.

The images we are viewing range in size quite a bit. However, we are looking for the server to help us with images that are over 100MB. That's when the download time becomes an issue from the standpoint of workflow.

BTW, we are running on a Windows server with the Apache Tomcat webserver. We also already have all of the database infrastructure in place. We're just looking for a way to serve up large image files efficiently.

Please let me know if you need any additional information. Thanks for your help.

sac

An example of what can be done with OMERO in a public setting with biological image data:

http://jcb-dataviewer.rupress.org/

What are the sort of 2D dimensions we're talking about here sac? 1Kx1K? 10Kx10K? Larger?

Thanks for the example. It looks very interesting. We have a range of file sizes, but a typical size might be on the order of 10K x 10K. Why do you ask?

sac wrote:Thanks for the example. It looks very interesting. We have a range of file sizes, but a typical size might be on the order of 10K x 10K. Why do you ask?

OMERO, at the moment, is by and large a planar system. As a result of the high dimensionality of a lot of biological image data our smallest "unit of work" for a lot of our visualization tools is what we call a section or a plane. One of the drawbacks of this sort of strategy is that very large 2D sections (like are present in your 10K x 10K images) aren't handled very well.

It's on our roadmap to deal with but it isn't something we support very well right now. Are you looking for something that just works out of the box? Perhaps we can work towards something that would suit your needs?

Thanks for the clarification. I'm not sure if it helps, but the largest files that we would normally see would be on the order of 500MB. If you go images in the GB range, it's just impractical to upload them to our server over the Internet.

In any case, even if we could share/view images that are in the 100MB - 200MB range, it would be worth looking at OMERO. It depends on how easily we can interface the OMERO server with our existing software. Ideally, the installation would be something like adding Windows Media or Real servers, but I suspect that may be wishful thinking. We are willing to struggle a bit with it a bit if the payoff is there for us.

We regularly deal with files that are many, many GBs in size and we certainly have remote visualization tools that can work on subsets of data. As far as integration goes, with OMERO.web and our rich Java client OMERO.insight I don't see any obvious blockers but I certainly can't speak concretely about what problems you might encounter specifically without more information.

OMERO is an enterprise application with many features for not just the sharing of image data but the management, analysis and general operating framework surrounding that data. Hence, it's not "next", "next", "next", "finish" and you're deployed I'm afraid, you're going to have to invest some time in OMERO as a solution.

What does need to happen in order for you to work with your 10K x 10K and larger datasets is for some work to be done to handle very large single planes of data. Is this something that you could help with?