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MIrax files

2013-03-11
2014-04-21
  • boskar
    boskar
    2013-07-01

    It might be a good idea to implement openslide as a backend.

    Whole slide scanners are becoming more and more popular, and community needs a good way to share scans.

    Now I'm using vips to convert it to pyramid tiff, and then serve it via iipserver. Unfortunately final performance seems to be worse, then proof-of-concept deepzoom_server.py from openslide-python, maybe due to disk nature of operations.

    Ofc iip definetely wins with scalability, and will probably be used anyway. On the other hand mrxs files are 10 times smaller, so depending on a hardware it might be faster to direct support openslide formats, then to use converted content.

     
  • Ruven
    Ruven
    2013-07-01

    Having taken a quick look at the Mirax docs http://openslide.org/formats/mirax/ isn't a Mirax file a collection of JPEG files like Deepzoom or Zoomify? If so, then I'm not sure what benefit there is from IIPImage reading such a file, as you can serve the JPEGs directly to a viewer, which would be much faster. This is also why they are so small compared to TIFF.

    What viewer are you using with IIPImage and your converted OpenSlide images?

     
  • boskar
    boskar
    2013-07-01

    It is not... In fact, internally it is, but from the users point of view MRXS as it is consist of .mrxs file, and a set of about 22 binary .dat files in a directory - one of the dat files is a set of jpeg, but It won't be easy to get them. The idea of serving them directly/after lossless transformation is interesting, but far too difficult to achieve.

    I'm using iipmooviewer via IIP, and openseadragon via DeepZoom, both from iipserver, and openseadragon from deepzoom_server.py.

    I've been trying to create static DeepZoom sets created with deepzoom_tile.py, but storing 332128 jpeg files (exactly) for one zoom level is far too much (especially when You want to serve more then 1000 slides).

     
  • Ruven
    Ruven
    2013-07-02

    OK, I see. It sounds like it could be possible to add this as a supported format. I'll look into this after iipsrv 1.0 is released.

    If anyone is interested in working on this, please let me know.

     
  • boskar
    boskar
    2013-07-04

    If testing counts - count me in! Unfortunately I can't code in C/C++.

    Anyway - I know at least one big project that could profit from openslide support, as but they are using Aperio format. ( http://node15.cci.emory.edu/CDSA/ - openseadragon/iipserver version is being made.)

     
  • Bob-O-Rama
    Bob-O-Rama
    2013-09-23

    Just curious: How does MIRAX differ from a JPG compressed, tiled. pyrimidal TIFF. which itself is an indexed collection of JPG encoded tiles?

     
  • Ruven
    Ruven
    2014-01-07

    This fork of iipsrv uses the openslide library to decode Mirax (and other formats). Has anyone tried this fork out? How well and efficiently does it work with Mirax files?

     

  • Anonymous
    2014-04-21

    I tried once again now - got stuck at compilation, as required openslide headers are not defined in autogen scripts, etc.
    I've managed to compile it a few months ago, but I can't get it working now. Although, I'm very interested in this feature. Could I open github issue for this?

     
  • boskar
    boskar
    2014-04-21

    Ok, so currently:

    CVT maximum viewport size set to 5000
    Full Request is DeepZoom=/home/patomorfa/sesja5/01_1.mrxs.dzi
    [1/1]: Command / Argument is DeepZoom : /home/patomorfa/sesja5/01_1.mrxs.dzi
    DeepZoom handler reached
    FIF handler reached
    FIF :: Image cache miss
    FIF :: OpenSlide image requested
    FIF :: Created image
    FIF :: Image dimensions are 4294967295 x 4294967295
    FIF :: Image contains 3 channels with 8 bits per pixel
    FIF :: Image timestamp: Tue, 04 Mar 2014 14:03:01 GMT
    FIF :: Total command time 183 microseconds
    DeepZoom :: DZI header request
    Memcached :: stored 306 bytes in 23 microseconds
    Total Request Time: 424 microseconds
    image closed and deleted
    Server count is 24
    

    and the output dzi file:
    /iipsrv/iipsrv4.fcgi?DeepZoom=/home/patomorfa/sesja5/01_1.mrxs.dzi

    <Image xmlns="http://schemas.microsoft.com/deepzoom/2008" TileSize="256" Overlap="0" Format="jpg">
    <Size Width="-1" Height="-1"/>
    </Image>
    

    so currently - not working for me with my raw sample.
    also: anonymous user was also me ; )

     
    Last edit: boskar 2014-04-21


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