Replies Created

  •
    MasoudR February 25, 2020 at 2:08 pm

    Dear Stephane,

    Loading a 32Bit Icy would work. However Icy starts up in 64Bit when it is installed without giving any option to choose.

    How would we load icy in a 32bit state while having both 32 and 64 bit javas installed?

     

    Thank you for the help,

    Masoud
    MasoudR July 5, 2019 at 3:31 pm

    Dear Stephane,

    Thank you for all the support.

    Sadly some of the people in my lab have not turned on the option to create the metadata files, is there any other way to open them?

    Does OME know about the issue with bio-formats? Could Icy use a previous version where the bug is not present until they fix it?

     

    Cheers,

    Masoud
    MasoudR July 4, 2019 at 11:24 am

    I just tried it with an older version of Icy: Icy 1.9.7.0

    With this, I can open my files. Using Seperate Files it gives me the series selection window, allowing me to open all files in a group.
    When using Group Files it gives me the tiled image again.

    With this, I can atleast analyse my data now using an older version. But it would be nice if this was fixed soon.
    MasoudR July 4, 2019 at 11:11 am

    Hello Stephane,

    Did you have any luck replicating the problems?

    I’ve tried opening my tif files with the “Seperate files” option now and it gives me another error:

    Java.lang.IndexOutOfBoundsException: Index 1 out-of-bounds for length 1
at java.base/jdk.internal.util.Preconditions.outOfBounds(Unknown Source)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Unknown Source)
at java.base/jdk.internal.util.Preconditions.checkIndex(Unknown Source)
at java.base/java.util.Objects.checkIndex(Unknown Source)
at java.base/java.util.ArrayList.get(Unknown Source)
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:688)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at plugins.kernel.importer.LociImporterPlugin.openReader(LociImporterPlugin.java:939)
at plugins.kernel.importer.LociImporterPlugin.open(LociImporterPlugin.java:853)
at icy.file.Loader.internalLoadSingle(Loader.java:3764)
at icy.file.Loader.loadSequences(Loader.java:3237)
at icy.file.Loader$5.run(Loader.java:2303)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

    They do open without error in imageJ
    MasoudR July 4, 2019 at 11:11 am

    Hello Stephane,

    Did you have any luck replicating the problems?

    I’ve tried opening my tif files with the “Seperate files” option now and it gives me another error:

    Java.lang.IndexOutOfBoundsException: Index 1 out-of-bounds for length 1
at java.base/jdk.internal.util.Preconditions.outOfBounds(Unknown Source)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Unknown Source)
at java.base/jdk.internal.util.Preconditions.checkIndex(Unknown Source)
at java.base/java.util.Objects.checkIndex(Unknown Source)
at java.base/java.util.ArrayList.get(Unknown Source)
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:688)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at plugins.kernel.importer.LociImporterPlugin.openReader(LociImporterPlugin.java:939)
at plugins.kernel.importer.LociImporterPlugin.open(LociImporterPlugin.java:853)
at icy.file.Loader.internalLoadSingle(Loader.java:3764)
at icy.file.Loader.loadSequences(Loader.java:3237)
at icy.file.Loader$5.run(Loader.java:2303)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

    They do open without error in imageJ

    One of my image stacks: https://ufile.io/lmgbqdvi
    MasoudR July 4, 2019 at 11:09 am

    Hello Stephane,

    Did you have any luck replicating the problems?

    I’ve tried opening my tif files with the “Seperate files” option now and it gives me another error:
    Java.lang.IndexOutOfBoundsException: Index 1 out-of-bounds for length 1
    at java.base/jdk.internal.util.Preconditions.outOfBounds(Unknown Source)
    at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Unknown Source)
    at java.base/jdk.internal.util.Preconditions.checkIndex(Unknown Source)
    at java.base/java.util.Objects.checkIndex(Unknown Source)
    at java.base/java.util.ArrayList.get(Unknown Source)
    at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:688)
    at loci.formats.FormatReader.setId(FormatReader.java:1397)
    at plugins.kernel.importer.LociImporterPlugin.openReader(LociImporterPlugin.java:939)
    at plugins.kernel.importer.LociImporterPlugin.open(LociImporterPlugin.java:853)
    at icy.file.Loader.internalLoadSingle(Loader.java:3764)
    at icy.file.Loader.loadSequences(Loader.java:3237)
    at icy.file.Loader$5.run(Loader.java:2303)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)
    They do open without error in imageJ

    One of my image stacks: https://ufile.io/lmgbqdvi