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    Josh Moore
    @joshmoore
    But imagine feeding them.
    Curtis Rueden
    @ctrueden
    @joshmoore I think it would be OK as long as you get re-merge as part of it. Then it's not that different from fork & pull.
    Josh Moore
    @joshmoore
    I think I’m going to have weird dreams now.
    Curtis Rueden
    @ctrueden
    :+1:
    Curtis Rueden
    @ctrueden
    @awalter17 @gab1one I fixed the ZCT issues! imagej/imagej-omero@725fdb6 :tada: :sparkles:
    I am waiting at EDI airport for our last passenger to arrive. Hopefully we'll ship out of here before 9:00 so that I don't miss @awalter17's talk. ^_^
    Gabriel Einsdorf
    @gab1one
    Awesome news! :D
    Curtis Rueden
    @ctrueden
    imagej-omero 0.5.2 + scifio 0.36.1 was uploaded to the OMERO-5.4 update site. I hope it is now working well enough for users these next couple of days. 🤞
    felix cc
    @fmeyenhofer
    it is thanks
    was just trying to get images from different groups than my default. here it says that the image id is not valid.
    I guess there would need be a parameter in the config dialog to set the group id of the omero session explicitly.
    Alison Walter
    @awalter17
    Ah yes, that's because we only ever use one SecurityContext which uses your default group. You're right we should probably offer that as a parameter. I'll make an issue in imagej-omero :smile_cat: Thanks @Meyenhofer!
    Alison Walter
    @awalter17
    imagej/imagej-omero#84
    Niko Ehrenfeuchter
    @ehrenfeu
    :heart:
    felix cc
    @fmeyenhofer
    @awalter17 :+1: (didn't see that)
    ah was just opened :smile:
    Curtis Rueden
    @ctrueden
    Curtis Rueden
    @ctrueden
    New ImageJ-OMERO released and uploaded. Includes a major fix to SCIFIO cell images; see imagej/imagej-omero#92. Run Help > Update... to receive it.
    I need help testing, especially on the server side. We need to ensure the scripts in the scripts directory of the imagej-omero repository all work as intended. I won't have time for a while to work on this project further.
    Curtis Rueden
    @ctrueden
    Best error received while testing ImageJ-OMERO: "error: communicator not destroyed during global destruction"
    Josh Moore
    @joshmoore
    That’s coming from deep in the Ice stack. If it’s happening in Java (as opposed to Python) then there may be a real instance leak.
    Curtis Rueden
    @ctrueden
    I saw it only once, at the conclusion of an omero script list run.
    So, not in Java.
    Josh Moore
    @joshmoore
    Then it’s coming from Python, which is thoroughly annoying but much less worrisome.
    Curtis Rueden
    @ctrueden
    That's good.
    Josh Moore
    @joshmoore
    Our hope is that Ice 3.7 will fix it.
    Gabriel Einsdorf
    @gab1one
    @awalter17 and I wrote a query that emulates "BrowseFacility.getImagesForDataset()" to be able to list images on the IDR. Because we found that method insufficiently slow, it took about 30 seconds just to get a list of about 20 images, the query took less than half a second.
    Is this a good idea or are we going to get into trouble with future omero versions
    Josh Moore
    @joshmoore
    I assume you’re using IQuery, eh? At some point far in the future it will go away, but at the moment it’s often still necessary. It’d be good to get anything you need into the facility though.
    ( ^ @gab1one )
    Gabriel Einsdorf
    @gab1one
    Yes IQueryPrx, ok that is good to hear, because now users can list the images from IDR within KNIME without hitting a timeout
    Josh Moore
    @joshmoore
    :+1: Did you try the getHierarchy methods?
    Gabriel Einsdorf
    @gab1one
    I tried, but as far as I understand it, it does not allow me to e.g. list all images in one specific dataset.
    I want to lazily represent the object tree (like in the web ui)
    Josh Moore
    @joshmoore
    (It may be a question of optimizing the server-side query)
    Gabriel Einsdorf
    @gab1one
    yes I think so, in my case I also only needed the name + id of the image so the ImageI I got from my query was enough
    Josh Moore
    @joshmoore
    :+1:
    Gabriel Einsdorf
    @gab1one
    The Facilities are much nicer to use though :)
    lorita
    @Lorita92_gitlab
    hello everyone! does anyone know how to open a psd file in image j? i already have downloaded jimi reader, jimi writer and jimi jar and pasted the files in the plugin area, but it doesn't work
    Josh Moore
    @joshmoore
    Hi @Lorita92_gitlab . This question is better asked on https://forum.image.sc/search?q=jimi Good luck.
    Curtis Rueden
    @ctrueden
    @/all I created the OMERO-5.5 update site, and uploaded SNAPSHOT versions of imagej-omero and imagej-omero-legacy that (theoretically) work with OMERO-5.5. If you use OMERO 5.5 and have time to test, that would be greatly appreciated. See also this Image.sc Forum thread.
    romainGuiet
    @romainGuiet

    Hi,
    I’m uploading an image on our OMERO server via a groovy script in ImageJ , and I would like to get the image ID of the uploaded file.
    I’m using the code example (see below)

      store = config.createStore()
        def reader = new OMEROWrapper(config)
    
        def library = new ImportLibrary(store,reader)
        def errorHandler = new ErrorHandler(config)
    
        library.addObserver(new LoggingImportMonitor())
        def candidates = new ImportCandidates (reader, paths, errorHandler)
        //println ( candidates ) 
    
        reader.setMetadataOptions(new DefaultMetadataOptions( MetadataLevel.ALL ) )
        def success = library.importCandidates(config, candidates)

    And I saw that it prints many info in the console (see below), but I didn’t find a way (yet ) to have access to it.

    OMERO Version: 5.4.9-ice36-b101
    Bioformats version: 6.3.1 revision: e355a853c5768721711cb9b29c3a27561539c4e4 date: 13 December 2019
    Attempting initial SSL connection to omero.epfl.ch:4064
    Depth: 4 Metadata Level: MINIMUM
    ZeissLSMReader initializing N:\0-PTS-OMERO\images\20200115_IN1_63x1.4_ccd_Image1_RG.lsm
    Reading LSM metadata for series #0
    1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 17ms. (18ms total) [0 unknowns]
    FILESET_UPLOAD_PREPARATION
    FILESET_UPLOAD_START
    Transferring N:\0-PTS-OMERO\images\20200115_IN1_63x1.4_ccd_Image1_RG.lsm...
    FILE_UPLOAD_STARTED: N:\0-PTS-OMERO\images\20200115_IN1_63x1.4_ccd_Image1_RG.lsm
    FILE_UPLOAD_COMPLETE: N:\0-PTS-OMERO\images\20200115_IN1_63x1.4_ccd_Image1_RG.lsm
    FILESET_UPLOAD_END
    IMPORT_STARTED Logfile: 17014
    METADATA_IMPORTED Step: 1 of 5  Logfile: 17014
    PIXELDATA_PROCESSED Step: 2 of 5  Logfile: 17014
    THUMBNAILS_GENERATED Step: 3 of 5  Logfile: 17014
    METADATA_PROCESSED Step: 4 of 5  Logfile: 17014
    OBJECTS_RETURNED Step: 5 of 5  Logfile: 17014
    IMPORT_DONE Imported file: N:\0-PTS-OMERO\images\20200115_IN1_63x1.4_ccd_Image1_RG.lsm
    Image:1095

    Thank you for your help,
    Romain

    jean-marie burel
    @jburel

    Hi Romain
    you could replace

    library.importCandidates(config, candidates)

    by

    containers = candidates.getContainers()
    index = 0
    containers.each() { c ->
            pixels = library.importImage(c, index, 0, 0)
            index++
           // pixels is a list from there you can then access the Image ID
        }

    I will update the example https://github.com/ome/training-scripts/blob/master/practical/groovy/crop_rectangle_from_image.groovy
    I hope it helps

    Jmarie

    romainGuiet
    @romainGuiet
    Thank you Jean-Marie! It helps a lot :D
    NicoKiaru
    @NicoKiaru
    Hi everybody, sorry for the very basic question, but what's the difference between the fiji plugin from omero (https://omero-guides.readthedocs.io/en/latest/fiji/docs/installation.html) and imagej-omero ?
    Curtis Rueden
    @ctrueden
    @NicoKiaru No need to apologize—it's confusing. I'll amend the readme of ImageJ-OMERO now to explain the difference, and paste the link here when ready.
    NicoKiaru
    @NicoKiaru
    :+1: thanks!
    Curtis Rueden
    @ctrueden
    @NicoKiaru The README has been updated. Please let me know if you still have questions about it.
    NicoKiaru
    @NicoKiaru
    I saw some changes in the branch pom-sj-29. By any chance, is imagej-omero working with recent clients now ?
    Curtis Rueden
    @ctrueden
    @NicoKiaru Unfortunately not—I just updated the location of the OMERO test infrastructure image to a new URL. But the code still needs more updating.