Release of Bio-Formats 5.2.2

bio-formats
Tags: #<Tag:0x00007fb87a4c2978>

#1

Dear All,

The bug-fix release Bio-Formats 5.2.2 is now available.

Improvements include fixes for three formats:

  • InCell - improved handling of Analyzer 2000 datasets to find TIFF files
  • FV1000 - fixed preview names ordering
  • OME-TIFF - enabled all BigTIFF extensions

Other improvements:

  • fixed a regression in which the DataTools number parsing API would not be thread-safe anymore

ImageJ/Fiji bug fixes and improvements:

  • fixed a bug when swapping dimensions of an image with multiple series of different dimensions
  • added an option to the exporter to pad filename indexes with zeros

Command-line tools improvements:

  • allowed the binaries to be symlinked (thanks to Gerhard Burger)
  • added an option to bfconvert to pad filename indexes with zeros

Full details can be found at
http://www.openmicroscopy.org/site/support/bio-formats5.2/about/whats-new.html

The software is available at:
http://downloads.openmicroscopy.org/bio-formats/5.2.2
and from the Java-8 update site for Fiji users.

Any problems or comments, please use the OME Forums or mailing lists:

Regards,

The OME Team


#2

Hi,

We are still having issues when saving data as .ids/.ics. We lose one slice after re-opening.

To replicate, open the Confocal Series file, and save at as IDS/ICS using Bio-Formats Exporter… then reopen the file.

We tried downloading Bio-Formats 5.1.10 to see if this could remedy the problem, from these links
http://downloads.openmicroscopy.org/bio-formats/5.1.10/

Downloading either bio-formats_plugins.jar and replacing it in plugins or gettingbioformats_package.jar still causes the same issue! So I do not understand where this is coming from… or are the previous versions in your website somehow also updated?

This is unfortunately a major problem for us, as the .ids/.ics format is one of the few that are universally read by most softwares and that have no size limitation, like TIFF, while keeping the metadata.

If someone could direct us in how to get the previous IDS/ICS functionality back, we would be very grateful!

Best

Oli


#3

Hi Oli,

We are currently working on a fix for the ICS Writer issue and have a PR open and reviewed which should make it into the next Bio-Formats release 5.2.3 which is currently scheduled for the end of the first week of October.

You can view the status of the open PR here - https://github.com/openmicroscopy/bioformats/pull/2566

In the meantime if you need to revert back to version 5.1.10 you can do so by replacing the Bio-Formats jars from the above link in both the plugins folder and also in the jars/bio-formats folder.

With Thanks,
David Gault


#4

By that do you mean the link I posted?

If so, I’d like to take this opportunity to go through the steps for this procedure here.

Right now inside the jars/bio-formats folder I have

formats-api-5.2.2.jar
formats-bsd-5.2.2.jar
formats-common-5.2.2.jar
formats-gpl-5.2.2.jar
jai_imageio-5.2.2.jar
mdbtools-java-5.2.2.jar
metakit-5.2.2.jar
ome-poi-5.2.2.jar
ome-xml-5.2.2.jar
specification-5.2.2.jar
turbojpeg-5.2.2.jar

I can download the following from the 5.1.10 page

loci_tools.jar
* formats-api.jar
* formats-bsd.jar
* formats-common.jar
* formats-gpl.jar
formats-bsd-test.jar
* ome-xml.jar
* specification.jar
** bio-formats_plugins.jar
* metakit.jar
bio-formats-testing-framework.jar

The ones with * are also in my jars folder, and the following jars do not have a download link.

jai_imageio-5.2.2.jar
mdbtools-java-5.2.2.jar
turbojpeg-5.2.2.jar
ome-poi-5.2.2.jar

I put the ** bio-formats_plugins.jar into the plugins folder, replacing bio-formats_plugins-5.2.2.jar

Now questions:

  1. The files without * (ie. with no equivalent file in the jars folder) are not necessary to download, correct?
  2. The missing files (jai_imageio-5.2.2.jar, etc...), should I leave them or remove them?

Remarks:

Whether I keep or delete the files for which I had no equivalent, Fiji would quit after displaying the Fiji logo.
Running it with the --debug flag gives

Error while executing the main() method of class 'net.imagej.Main':
java.lang.IllegalArgumentException: Invalid service: io.scif.ome.services.DefaultOMEMetadataService
        at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
        at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
        at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
        at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
        at org.scijava.Context.<init>(Context.java:278)
        at org.scijava.Context.<init>(Context.java:234)
        at org.scijava.Context.<init>(Context.java:174)
        at org.scijava.Context.<init>(Context.java:160)
        at net.imagej.ImageJ.<init>(ImageJ.java:76)
        at net.imagej.Main.launch(Main.java:61)
        at net.imagej.Main.main(Main.java:68)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
Caused by: java.lang.NoClassDefFoundError: loci/formats/FormatException
        at java.lang.Class.getDeclaredConstructors0(Native Method)
        at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
        at java.lang.Class.getConstructor0(Class.java:3075)
        at java.lang.Class.newInstance(Class.java:412)
        at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:302)
        at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
        ... 17 more
Caused by: java.lang.ClassNotFoundException: loci.formats.FormatException
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 23 more

The only solution I have for now is to use the bio-formats folder and the bio-formats_plugins.jar from an old installation of Fiji… But any explanation on how to perform a ‘clean’ revert would definitely be appreciated.


#5

Yes that was the correct link posted. Normally it wouldn’t be recommend to downgrade in this manner and using an older Fiji install would probably be the cleanest way to revert backwards. If you are comfortable enough replacing the jars it can be used as a temporary fix until the newt release is available.

The files without * (ie. with no equivalent file in the jars folder) are not necessary to download, correct?

No, theres no need to download those, only the files that were originally present

The missing files (jai_imageio-5.2.2.jar, etc…), should I leave them or remove them?

The missing files you can leave the original versions as they are


#6

Dear @dgault,
Thanks for the info, but what about the error I get when doing the procedure that does not involve getting an older version of Fiji?


#7

A simpler procedure for downgrading:

  • Delete jars/bio-formats/* and plugins/bio-formats_plugins*.jar.
  • Download bioformats_package.jar of the desired version and place into your plugins folder.

When you want to go back to normal, delete bioformats_package.jar and run Help :arrow_forward: Update… to restore the missing Bio-Formats component JARs.


#8

Dear @ctrueden

Thank you for the info, this worked just fine!


#9

This is a known issue when certain Bio-Formats JARs are missing. See e.g. scifio/scifio#18.

At the moment, you can avoid the issue using the following command line invocation:

ImageJ-linux64 -Dscijava.context.strict=false --

Where ImageJ-linux64 is the executable for your installation of Fiji.

You will still see errors in the console, but it will be possible to launch Fiji and use the updater to repair the installation.

The launcher really should enable this non-strict mode by default (see imagej/imagej-launcher#28) but at the moment, it still does not.

SciJava Common 3 will very likely set non-strict mode by default.


#10

The 5.2.3 release of Bio-Formats fixes this.


#11

Since the Bio-Formats update, when importing .czi images the different channels are all importing as a single color (visually - they are still independent channels). The easy work-around is to split and re-merge the channels, but just wanted to alert someone to this new issue since the update.

Edited: my mistake. I thought this was the most recent Bioformats update. This new problem manifested July 2017, and is probably not applicable here. Apologies.


#12

Hi @mfacette

It may simply be that the Bio-Formats importer is set to use the Composite color mode. At the bottom of the Bio-Formats Importer options window you should be able to change the color mode to your choosing.

If that is not the problem would you be able to upload a sample file for testing to https://www.openmicroscopy.org/qa2/qa/upload/

David Gault


#13

Ah, this was exactly the problem - I feel so silly! Thank you!