saving a huge file

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  • Antonin Broz October 21, 2019 at 6:08 pm

    Hello,

    I am trying to save a very big tiff image (24GB) on a SSD disk and it takes “forever”, although loading the file (.ims) from the disk is quite swift. I understand that such a file must take some time to save but I have noticed that only one CPU core is used during the saving and I have 32 threads (16 physical cores) at my disposal. The disk is not writing at its maximum speed. Do you have any idea where the problem lies?

    Best regards,

    Tony

    Stephane Dallongeville October 22, 2019 at 11:19 am

    Hi Tony,

    We are using Bio-Formats internally to save TIFF file as we always save in OME-TIFF format to preserve all information (dimension and metadata). The problem is that indeed Bio-Formats OME-TIFF saving operation is *very* slow. We will try to find solutions to make it faster if possible on our side (using multi-threading for instance) as this is an old issue which become more and more harmful with bigger images.

    Best,

    – Stephane

    Antonin Broz October 22, 2019 at 11:45 am

    Hi Stephane,

    thanks for the quick answer. Unfortunatelly, the file saving after analysis in IJ or Icy is the most time consuming part of the image processing. But the softwares and Bioformats plugin are free, so please do not take my question as a complaint. 🙂 I was just wondering if I am doing something wrong. Thanks a lot for your effort!

    Regards,

    Tony

    Stephane Dallongeville October 22, 2019 at 11:50 am

    No worries really we understand that is an important issue 😉 Fiji also use Bio-Formats internally so i guess the saving time is about the same as soon you try to save in OME-TIFF. Classic TIF should be faster but it won’t preserve all information that you probably need here.

    Best,

    – Stephane

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