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    Curtis Rueden
    @ctrueden
    For now I just removed all those links. Seems a shame though.
    H Flynn
    @hflynn
    @ctrueden The FAQ pages were legacy from when the documentation was much sparser. They were removed nearly 2 years ago to reduce the maintenance burden - all the relevant info is in the documentation now.
    Curtis Rueden
    @ctrueden
    FYI, the BoneJ2 developer @rimadoma has ported the BoneJ support for Scanco ISQ to SCIFIO (scifio/scifio#337). However, this poses a question about licensing of PFF reader implementations in SCIFIO. Just wanted to draw your attention to the discussion: https://github.com/scifio/scifio/pull/337#issuecomment-274087843
    Robert Haase
    @haesleinhuepf
    Hey guys, I'm using BioFormats to save TIF files and it works like a charm! However, there are hundreds of messages coming out to the command line like "21:29:32.546 [main] DEBUG loci.formats.tiff.TiffSaver - Writing tile/strip 35/100 size: 227 offset: 770691". Is there a way to turn this logging of (something like LOGGER.setDebug(off)))? Thanks!
    Curtis Rueden
    @ctrueden
    @haesleinhuepf How are you saving them? CLI tool? Something else?
    Robert Haase
    @haesleinhuepf
    Curtis Rueden
    @ctrueden
    The best way to disable those log messages is, in my experience, to figure out how they got turned on in the first place. And NOT to make some hardcoded API call.
    Robert Haase
    @haesleinhuepf
    This is the only place in the code where BioFormats is used... I just introduced the bioformat dependency to make the Tiff-writing work
    Curtis Rueden
    @ctrueden
    What is your runtime environment? Main method in IDE? Fiji? Something else?
    Robert Haase
    @haesleinhuepf
    It happens in IntellliJ and on gradle test
    Curtis Rueden
    @ctrueden
    Bio-Formats uses a logging framework. See https://imagej.net/Logging
    Is there another dependency with a logback or log4j configuration file embedded in it?
    Robert Haase
    @haesleinhuepf
    There is no other dependency. If I comment out Bioformats in my build.gradle, the log4j dependency disappears from my dependency tree
    Curtis Rueden
    @ctrueden
    There could still be a config file somewhere. It's just a resource on the classpath.
    If you find a way to debug logback/log4j config, that would be a great addition to the Logging page.
    Robert Haase
    @haesleinhuepf
    how could be the log4j config file name?
    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.