[ome-devel] OMERO.figure limitations

[Christophe TREFOIS]

Dear Will,

It worked partially.

We will create a bug submission on the github page shortly.

The quick breakdown is that the page size can be smaller than the imported image resulting in a silent error.
Eg, the javascript complains about some negative x-y values.

To make it work, we simply have to increase the page size to something bigger and then it works perfectly.

My colleague Yohan Jarosz created a pull request for this by adding more paper formats in the dropdowns of the Django templates.

Best,

From: William Moore [mailto:will at lifesci.dundee.ac.uk]
Sent: jeudi 30 octobre 2014 00:40
To: Christophe TREFOIS
Cc: ome-devel at lists.openmicroscopy.org.uk
Subject: Re: [ome-devel] OMERO.figure limitations


Hi Christophe,

 Since OMERO.figure does not feature a tiled image viewer, it only works with
single planes of the whole image at a time.
Therefore, this limits the size of images that can be loaded.

However, there is no strict limit on the maximum size that can be used.
We can load entire planes larger than the "Big Image" threshold where images
become tiled in OMERO.

Currently, I've chosen an arbitrary limit of 5000 x 5000 pixels (or equivalent) since 4k x 4k images
seemed to work OK.
This is hard-coded, E.g. in the 1.0.0 release it's at:

https://github.com/will-moore/figure/blob/develop/static/figure/js/figure-1.0.0.js#L2621

if (data.size.width * data.size.height > 5000 * 5000) {
    alert("Image '" + data.meta.imageName + "' is too big for OMERO.figure");
    return;
}

You could try to increase this limit in figure/static/figure/js/figure-1.0.0.js
to see if 5000 x 10000 image planes can be loaded.

Perhaps you can try this first...

Log in to the web client and find an example image of 10000 x 5000 pixels.
Then edit <your-server> and <image-id> in this url
to load an entire plane.
  <your-server>/webgateway/render_image/<image-id>/0/0/

This will give you some idea of the performance of this.
If performance is not too bad, then feel free to increase the limit above,
although bear in mind that performance will be worse at locations with lower bandwidth.


To fully support large tiled images in OMERO.figure, we'd need a proper tile-based
image viewer. But this would be quite a lot of work.

One alternative is for your users to draw rectangle ROIs on their big images in Insight
(ROIs of 3000 x 3000 or less) then use the script:
util script > Images From ROIs
to create new images based on those regions. These can then be imported into OMERO.figure.

 Hope that helps,

   Will.



On 29 Oct 2014, at 17:32, Christophe TREFOIS <christophe.trefois at uni.lu<mailto:christophe.trefois at uni.lu>> wrote:


Dear all,

Does anybody know the limitation in terms of pixel size of OMERO.figure ?

Our researchers love this new tool but sometimes use stitched images which can be around 10.000 x 5.000 pixels which doesn't seem to work with OMERO.figure.

Can this setting be changed anywhere?

Best,

................................................................................
Dr. Christophe TREFOIS, Dipl.-Ing.
Doctor in Biology
Senior Technical Specialist
UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | House of Biomedicine
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T +352 46 66 44 6124
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