Error using bioformats with czi images

bio-formats
imagej

#1

Hello !
I have beginner question about bioformat concerning czi files. I try to read some metadata in my file and i start using ImageReader(). I have no problem with tiff files, but with czi i got the following one :

14:48:30.820 [main] DEBUG loci.formats.FormatHandler - 3i SlideBook SlideBook6Reader library not found. Please see http://www.openmicroscopy.org/site/support/bio-formats/formats/3i-slidebook.html for details.
java.lang.UnsatisfiedLinkError: null
at loci.formats.in.SlideBook6Reader.(SlideBook6Reader.java:90) ~[formats-gpl-5.1.5.jar:5.1.5]
at java.base/java.lang.Class.forName0(Native Method) [na:na]
at java.base/java.lang.Class.forName(Class.java:291) [na:na]
at loci.formats.ClassList.(ClassList.java:127) [formats-api-5.1.5.jar:5.1.5]
at loci.formats.ClassList.(ClassList.java:85) [formats-api-5.1.5.jar:5.1.5]
at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:78) [formats-api-5.1.5.jar:5.1.5]
at loci.formats.ImageReader.(ImageReader.java:115) [formats-api-5.1.5.jar:5.1.5]
at gred.nucleus.test.bioformatTest.main(bioformatTest.java:41) [classes/:na]
14:48:31.028 [main] DEBUG loci.common.NIOByteBufferProvider - Using mapped byte buffer? false
14:48:31.040 [main] INFO loci.formats.ImageReader - ZeissCZIReader initializing /home/user/etc/ImageTEST/20180919_psf_63x_b_z 0_2-04_STACK13-25.czi
14:48:31.041 [main] DEBUG loci.formats.FormatHandler - ZeissCZIReader initializing /home/user/etc/ImageTEST/test_bille/20180919_psf_63x_b_z 0_2-04_STACK13-25.czi
14:48:31.041 [main] DEBUG loci.formats.FormatHandler - loci.formats.in.ZeissCZIReader.initFile(/home/user/etc/ImageTEST/20180919_psf_63x_b_z 0_2-04_STACK13-25.czi)
14:48:31.137 [main] INFO loci.formats.FormatHandler - Unknown segment type: MM * �

I checked http://www.openmicroscopy.org/site/support/bio-formats/formats/3i-slidebook.html , so should i convert my files in tiff to get my information ?

Best ,

Tristan


#2

Hi @Titus,

sorry for the delay here. Although fairly verbose, most of the [logging information in the console](see https://imagej.net/Logging) about the 3i Slidebook reader is displayed at the DEBUG level and should be safe to ignore.

Are you encountering specific issues related to the reading of your .czi files? If that’s the case, the logging indicates you are used an old version of Bio-Formats 5.1.5. If you can afford to download the version bundled in the Java-8 update site, there have been substantial improvements made to this particular reader over the last 3 years

Best,
Sebastien


#3

Hi ,

Thank you Sebastien, it’s looks like working with a more recent version but only if i have the jar in local importation. When i’m using the import by maven my problem is sill there even if i use a more recent version…
Thank you for the DEBUG level suggestion I will check it.

Best,

Tristan


#4

Hi ,
I solved partially my problems. At the end I used loci_plugins in version 5.0.0-beta1 and read my images with BF.openImagePlus().
I have 2 different images coming from the same LSM 800 microscope and i can read metadata for one but for the other one I have the following error :

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
	at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
	at java.base/java.util.Objects.checkIndex(Objects.java:372)
	at java.base/java.util.ArrayList.get(ArrayList.java:458)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:455)
	at loci.formats.FormatReader.setId(FormatReader.java:1333)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
	at loci.plugins.BF.openImagePlus(BF.java:95)
	at loci.plugins.BF.openImagePlus(BF.java:80)
	at gred.nucleus.test.bioformatTest.main(bioformatTest.java:50)

I check my images, their are different because I got 4 channels for one and only 1 channel the other one etc. I’m a bit confuse for the origin of this problem. I saved my image bugging as a tiff and it’s working …
I don’t really know how to identify the problem. Could it come from a specific metadata field present in my image which bug ? Or a way of acquisition ? or the way the image is save ?

Best,

Tristan