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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Dear All-<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">My apologies to our colleagues at RIKEN—in our discussion, I should have mentioned BD5, which is their implementation of HDF5 for bioimaging data. See:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><a href="https://github.com/openssbd/BDML-BD5">https://github.com/openssbd/BDML-BD5</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><a href="http://ssbd.qbic.riken.jp/bdml/bd5.html">http://ssbd.qbic.riken.jp/bdml/bd5.html</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Cheers,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Jason<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk>
<b>On Behalf Of </b>Manuel Stritt<br>
<b>Sent:</b> 18 October 2018 18:13<br>
<b>To:</b> OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>
<b>Subject:</b> Re: [ome-users] HCS File Format / HDF5<o:p></o:p></span></p>
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<p class="MsoNormal">Dear Sebastien & OME Team,<o:p></o:p></p>
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<p class="MsoNormal">thanks for the great summary of all this info and pointers.<o:p></o:p></p>
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<p class="MsoNormal">Based on that we'll have some internal discussions and see how we will handle that - maybe <o:p></o:p></p>
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<p class="MsoNormal">we can find a way to contribute <a href="http://s.th">s.th</a>. an push things forward.<o:p></o:p></p>
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<p class="MsoNormal">The main question seems to be how to get the output of (all!) HCS readers into a standardized<o:p></o:p></p>
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<p class="MsoNormal">container format.<o:p></o:p></p>
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<p class="MsoNormal">Mario mentioned speed and disk-space. In addition to that I have in mind that we might<o:p></o:p></p>
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<p class="MsoNormal">do some computation in the cloud and therefore transferring some data on-demand into the cloud.<o:p></o:p></p>
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<p class="MsoNormal">Having all data of one plate in one file would be very handy for that and eliminate latency problems.<o:p></o:p></p>
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<p class="MsoNormal">I'll keep you updated...<o:p></o:p></p>
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<p class="MsoNormal">Regards,<o:p></o:p></p>
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<p class="MsoNormal">Manuel<o:p></o:p></p>
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<p class="MsoNormal">On Wed, Oct 17, 2018 at 10:22 AM Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk">s.besson@dundee.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi Manuel and Mario,<br>
<br>
From the OME side, here are a couple of pointers on open HCS/HDF5-based formats and their compatibility.<br>
<br>
The open CellH5 format developed by EMBL [1] is currently supported by Bio-Formats [2]. Data stored in this<br>
form can be read by our APIs and managed in an OMERO server. Bio-Formats also has support for writing<br>
CellH5 files as a writer which was contributed by the developers of the format alongside the reader.<br>
<br>
Re OME and HDF5, since the beginning of the year we have been modernizing our open file formats in order<br>
to offer support for modalities like multi-resolution images and add support for new performant binary data<br>
containers. This is part of a larger strategy that OME has embarked on where we explicitly work to support a<br>
range of binary containers, in order to address the issues created by the growing number of imaging modalities<br>
that generate large, complex multi-dimensional data. For example, we are currently extending our OME-TIFF<br>
specification to support pyramidal levels and will soon release open readers and writers for these formats. This<br>
work targets the rapidly emerging whole slide imaging and digital pathology community.<br>
<br>
We have also explored adding support for binary vessels like HDF5, KLB and others. Part of this work was<br>
presented during the 2018 OME Users meeting [3]. This work results from an intersection of our desire to expand<br>
support for binary vessels and the requirement to support datasets that will soon be published in IDR [4]. HDF5<br>
has several advantages (Mario has discussed these), but a full implementation requires the development of yet<br>
another file format (YAFF), something that is anathema to OME’s philosophy. There are already useful<br>
implementations of HDF5, e.g., BigDataViewer [5] that we aim to support in Bio-Formats. Regardless, writing<br>
an HDF5-based format requires substantial work. A full technical proposal [5] details the series of changes that<br>
need to happen at the model and API level to make this happen. Unlike the OME-TIFF pyramidal work, full<br>
support for an OME-HDF5 or any other new binary vessel will necessitate breaking changes across our entire<br>
software including a new OME Data Model. We will keep reporting on the progress via blog posts as well as<br>
during our next Users Meeting.<br>
<br>
Best,<br>
Sebastien, Jason & The OME Team<br>
<br>
<br>
[1] <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3673213/" target="_blank">
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3673213/</a><br>
[2] <a href="https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/cellh5.html" target="_blank">
https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/cellh5.html</a><br>
[3] <a href="https://downloads.openmicroscopy.org/presentations/2018/Users-Meeting/Workshops/NewFileFormats/BinaryVessels/" target="_blank">
https://downloads.openmicroscopy.org/presentations/2018/Users-Meeting/Workshops/NewFileFormats/BinaryVessels/</a><br>
[4] <a href="https://www.cell.com/cell/pdf/S0092-8674(18)31243-1.pdf" target="_blank">
https://www.cell.com/cell/pdf/S0092-8674(18)31243-1.pdf</a><br>
[5] <a href="https://github.com/bigdataviewer" target="_blank">https://github.com/bigdataviewer</a><br>
[6] <a href="https://docs.google.com/document/d/1vCtIrxtlbA-SWPJVzwHOSnbfkbGKJAbijhvhvlSLMEw/edit#heading=h.r20td2bzgkgw" target="_blank">
https://docs.google.com/document/d/1vCtIrxtlbA-SWPJVzwHOSnbfkbGKJAbijhvhvlSLMEw/edit#heading=h.r20td2bzgkgw</a><br>
<br>
> On 11 Oct 2018, at 15:45, Manuel Stritt <<a href="mailto:manuel.stritt@idorsia.com" target="_blank">manuel.stritt@idorsia.com</a>> wrote:<br>
><br>
><br>
> Dear Mario,<br>
><br>
> thanks a lot for the detailed explanation with concrete measurements, very valuable!<br>
><br>
> So did you / someone try CellH5 or did you use your own HDF5 structure ?<br>
><br>
> Any plans and/or recommendations from OME side for bioformats/Omero integration?<br>
><br>
> Regards,<br>
> Manuel<br>
><br>
><br>
> Dear Manuel,<br>
><br>
> On 10.10.2018 08:46, Manuel Stritt wrote:<br>
> > Dear all,<br>
> ><br>
> > we're currently rethinking our high content screening workflow and thus I'm thinking about a good way to store all data.<br>
> > My idea is to create one e.g. HDF5 file per plate which contains all the images + meta data.<br>
> > Do have any recommendations regarding that (I think Mario once triggered a discussion around that topic) ?<br>
> ><br>
> > If some kind of HDF5 is considered as solution - then still a structure specification would be needed.<br>
> > Kai and Nico mentioned the CellH5 format, a flavor of HDF5.<br>
> > As far as I can see this is supported by bioformats / Omero. However, it's still unclear how<br>
> > to pack the output of a e.g. Opera machine into a CellH5 format in a convenient way.<br>
> ><br>
> > In addition there was a discussion about an official OME-HDF5 format, right?<br>
> > What's the current status for that?<br>
><br>
> In our testing, the containers provide a big benefit for the file<br>
> system and storage back end, especially when a large NAS storage is<br>
> used. For a typical desktop application with a local spinning disk,<br>
> there was virtually no difference in speed or file system overhead.<br>
><br>
> On a NAS, we got a 30% eduction in storage space due to reduced chunk<br>
> size overhead. This is a tunable parameter, so your mileage may vary!<br>
> It may be anything between 0% and up to 50% (or more) reduction,<br>
> depending on your image file size and the file system chunk size.<br>
><br>
> Furthermore we got significantly faster data transfer rates because<br>
> the data is more consecutive. An rsync transfer of a full plate from/to<br>
> the NAS was about twice as fast when transferring the container than<br>
> the individual files.<br>
><br>
> Last not least the container can apply transparent compression without<br>
> modifying the original file, so you can (transparently) apply bzip2 or<br>
> other compression schemes on the raw file, while keeping the full<br>
> (proprietary) file intact and unchanged.<br>
><br>
><br>
> All this comes also at a price. There where situations where we would<br>
> have liked to access images and it was not as easy as we hoped. Its<br>
> good if the database supports download of individual files, to make<br>
> the image access transparent for end users. But when the database is<br>
> down, image access becomes quite hard for end users. Furthermore, there<br>
> is a unlucky number of ~100-1000 files where access is always a hazzle,<br>
> because manual download becomes too cumbersome and container extraction<br>
> is typically not super comfortable.<br>
><br>
> Long story short: containers are great, but I would really love to<br>
> see them in combination with a simple, graphical, cross-platform file<br>
> management utility that allows adding and extracting files. There are<br>
> some such utilities like HDF5View [1] but they are not yet comparable<br>
> to something like WinZip/WinRAR/7Zip/...<br>
><br>
> [1] <a href="https://support.hdfgroup.org/HDF5/Tutor/hdfview.html" target="_blank">
https://support.hdfgroup.org/HDF5/Tutor/hdfview.html</a><br>
><br>
> Viele Gruesse,<br>
><br>
> Mario Emmenlauer<br>
><br>
><br>
> --<br>
> BioDataAnalysis GmbH, Mario Emmenlauer Tel. Buero: +49-89-74677203<br>
> Balanstr. 43 mailto: memmenlauer * <a href="http://biodataanalysis.de" target="_blank">
biodataanalysis.de</a><br>
> D-81669 München <a href="http://www.biodataanalysis.de/" target="_blank">
http://www.biodataanalysis.de/</a><br>
><br>
><br>
><br>
><br>
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