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    Curtis Rueden
    @ctrueden
    There are lots. I would mvn dependency:copy-dependencies && for f in target/dependency/*.jar; do jar tf "$ f" | grep log; done to see what shows up.
    $f argh mobile autocorrect.
    Robert Haase
    @haesleinhuepf
    While debugging, I just found out, that the log4j internal log level is null...
    Curtis Rueden
    @ctrueden
    I have noticed debug mode mysteriously turn on in other situations too and never made time to track down why. So keep us posted on any findings please!
    Robert Haase
    @haesleinhuepf
    Ok, I'll continue tracing and let you know! But thanks so far! :)
    Muad Abd El Hay
    @Cumol
    What does the conversion speed of bfconvert (form the tools) depend on? I have long time series (18k images) that need to be combined and converted to .tiff. Right now it is taking 45 minutes per dataset. Is something going wrong?
    Jan Eglinger
    @imagejan
    @Cumol this forum thread about slow tiff writing might be related
    Muad Abd El Hay
    @Cumol
    Thanks for the link @imagejan. Seems like an open issue. I wonder if it was introduced with the last update
    Niko Ehrenfeuchter
    @ehrenfeu
    @Cumol the conversion speed depends (at least in my experience) heavily on the I/O speed of the storage. So if your input and / or output files are e.g. on a network share, it will be orders of magnitude slower than on local disks for example...
    Muad Abd El Hay
    @Cumol

    @ehrenfeu Ah, that explains a lot. It is probably faster to convert locally and then move to a network share.

    I wonder thought why ImageJ seems to be doing just find with the task. Loading the images as virtual stack and then writing them as .tiff

    Niko Ehrenfeuchter
    @ehrenfeu
    Virtual stack is not loading the entire dataset upfront, but only during processing. If you plainly "save" as TIFF in ImageJ (as opposed to using the Bioformats exporter) it is saving as a normal TIFF (without all the benefits of OME-TIFF) which is a lot faster but at the cost of losing metadata.
    Muad Abd El Hay
    @Cumol
    In which situations do I need the metadata?
    Niko Ehrenfeuchter
    @ehrenfeu
    I would rather turn that question around - in what situations is it acceptable to discard the metadata?
    Muad Abd El Hay
    @Cumol

    The original metadata are in the raw files, so they can always be read. But for downstream manipulation/analysis (in my case converting to tiff, merging into one file, converting that into hdf5 and then using an analysis pipeline that has troubles dealing with TIFF files that include metadata).

    What is the added value to have the metadata in the .tiff or hdf5 file?

    Maybe I do not understand what kind of metadata is stored in a .ome.tiff file. Do you have a link that explains the importance of them?

    Niko Ehrenfeuchter
    @ehrenfeu
    Well, if your downstream processing involves multiple conversion steps (which sometimes can't be avoided, I know...), you'll most likely reduce the preserved Metadata anyway in one of them. As you are aware that it is important to keep your raw data, that seems okay to me. I would check if the conversion results at least preserve the spatial calibration (pixel size etc) to make sure that size measurements will be correct.
    About the details of the Metadata in OME-TIFF, maybe someone from the openmicroscopy staff would be able to provide a good link with explanations...?
    Curtis Rueden
    @ctrueden
    I forgot: is there is a way to link to the latest version of a Bio-Formats documentation page, so instead of e.g. https://docs.openmicroscopy.org/bio-formats/5.9.0/users/imagej/load-images.html#using-bio-formats-to-load-images-into-imagej, we get that information but for the most recent release?
    Josh Moore
    @joshmoore
    /bio-formats/$version/ —> /latest/bio-formats/
    Curtis Rueden
    @ctrueden
    @joshmoore Thanks!
    Josh Moore
    @joshmoore
    De nada.
    Curtis Rueden
    @ctrueden
    I am nearly done retiring the LOCI Trac instances. The public LOCI Software Trac is now archived here: https://uw-loci.github.io/tickets/
    I should have redirects from dev.loci.wisc.edu/trac/software/... to the right places very soon.
    I mention it here because nearly all of the tickets are Bio-Formats-related.
    Josh Moore
    @joshmoore
    :+1: thanks, Curtis. Probably will need to do the same for our instance soon.
    Curtis Rueden
    @ctrueden
    Let me know when you do; there are a lot of http://trac.openmicroscopy.org.uk/ome/intertrac links I'll need to fix then.
    (Unless you plan to keep those working.)
    Josh Moore
    @joshmoore
    Hmmm.... interesting. I'll have to check. Do you have a pointer to one?
    Curtis Rueden
    @ctrueden
    If you git clone git://github.com/uw-loci/tickets and then git grep trac.openmicroscopy you'll see 119 examples. :wink:
    There are some in https://github.com/imagej/tickets, the other Trac instance, as well.
    Josh Moore
    @joshmoore
    One of those links looks to already be broken :( We'll try to fix via a redirect.
    Cool, thanks.
    Curtis Rueden
    @ctrueden
    FYI, netcdf-java v5.0.0 was recently released: https://github.com/Unidata/netcdf-java/releases/tag/v5.0.0
    Josh Moore
    @joshmoore
    thanks. I passed the info along.
    NicoKiaru
    @NicoKiaru

    I'm sttrugling a bit with something that looked simple... Maybe you can help me ? Basically I want to use the [https://github.com/ome/bioformats/blob/develop/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java] (ImageConverter) class within a Fiji plugin. Which dependency should I declare within my pom file ? I tried:

            <dependency>
                <groupId>ome</groupId>
                <artifactId>pom-bio-formats</artifactId>
                <version>6.2.0</version>
            </dependency>

    Which is in the Scijava Maven repository, but apparently IntelliJ do not find the ImageConverterclass. I'm a bit out of options right now...

    Josh Moore
    @joshmoore
    To do the same, I use bio-formats-tools. See https://github.com/spacetx/spacetx-writer/blob/master/build.gradle#L32, but note that that's a duplicate. The version from the ome/bioformats repository has not yet been removed.
    NicoKiaru
    @NicoKiaru
    Yeepee! Thanks @joshmoore . I do not really understand the logic behind, but at least I can work with that.
    Josh Moore
    @joshmoore
    :+1: If you run into any problems, perhaps open issues against https://github.com/ome/bio-formats-tools/issues -- I know of a few off the bat, like the constructor is private.
    (issues or PRs of course ;) )
    NicoKiaru
    @NicoKiaru
    Oki doki, I'll try the to use the main method first, which is public. I'll let you know how that goes ;-)
    Josh Moore
    @joshmoore
    (That's what I did as well.) Good luck.
    NicoKiaru
    @NicoKiaru
    Aaah, just found out there's no pyramid option in this package. Is there a way to have a version with it ? It seems pyramid options are only in the develop branch...
    Ah sorry there is... I have probably another problem is my function call. I'll dig
    Curtis Rueden
    @ctrueden
    We need a shovel award, for people like @NicoKiaru. Every time you dig and report back your findings, you earn points. These go on your CV and employers take it more seriously than journal impact factor. </daydream>
    NicoKiaru
    @NicoKiaru
    Ahahah I need a shovel to hide right now. Just found out I forgot to remove a space in the ' -pyramid-scale' argument. I had to go full debug to find out this string is not equal to '-pyramid-scale'.
    Curtis Rueden
    @ctrueden
    At least it only took a few minutes to solve!
    Josh Moore
    @joshmoore
    Cheers.
    Curtis Rueden
    @ctrueden
    FYI, netCDF Java developers are looking for feedback on their new public API.
    Josh Moore
    @joshmoore
    Thanks, @ctrueden. :thumbsup: