Open Microscopy Environment

Dear all,

I'm very sorry to report that 3i has released a new version of its SlideBook software (v5.5) that changes the .sld file format. Current BF-importer in FiJi crashes when trying to read such files. Since the software now has an option "Save as SlideBook 5.0 sld" I don't think this is a duplicate of #9933, but I'm not 100% sure about this.

An example file from the new SlideBook version is attached (very small, just 76x80x1, 1ch, 1t).

Let me know if we can provide more help for this!

Cheers
Niko

Hello Niko,

Thanks for this. We will check the file and either expand the existing 9933 ticket or create a new one.

Cheers,

Andrew

Hi Niko,

As always, thanks for this.

I assume that you see something like this when attempting to open the file in Fiji:

Code: Select all

Exception in thread "main" loci.formats.UnknownFormatException: Unknown file format: SlideBook_5.5_crop.sld
   at loci.formats.ImageReader.getReader(ImageReader.java:192)
   at loci.formats.ImageReader.getFormat(ImageReader.java:159)
   at loci.formats.tools.ImageInfo.configureReaderPreInit(ImageInfo.java:388)
   at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:984)
   at loci.formats.tools.ImageInfo.main(ImageInfo.java:1031)


This is part of the problem:

http://trac.openmicroscopy.org.uk/ome/ticket/9933

But the bigger issue at the moment is that the "magic byte" identifiers have changed between 5.0 and 5.5, so Bio-Formats doesn't know that this is a Slidebook file at all. New ticket filed here (and you have been CC'd):

https://trac.openmicroscopy.org.uk/ome/ticket/10473

Regards,
-Melissa

Right, that's exactly what I got.

As always, thanks Melissa (and Andrew of course).

Cheers,
~Niko

According to the trac ticket the Slidebook 5.5 format reading was fixed a month ago, but even having the latest LOCI plugins in FiJi I still can't open them.

Do you know when to expect the updated BioFormats reader in FiJi? I even have the LOCI repository in my FiJi installations, but it didn't help.

Sorry for being so impatient

Hi,

This should be available quite soon; the next (4.4.7) point release of Bio-Formats should be made in the next week or so.

In the meantime, you can if you wish update the .jar files FiJi is using from, for example, http://hudson.openmicroscopy.org.uk/view/2.%20Stable/job/BIOFORMATS-stable/lastSuccessfulBuild/artifact/artifacts/. Note that FiJi has a number of separate jar files in the "jars" and "plugins" directories, and you'll need to replace all of them or it will break things [scifio*.jar, ome*.jar, loci*.jar, bio-formats.jar etc.]


Regards,
Roger

Thanks Roger, I'll try that.

I completely failed to update the BF jars manually, ending up in a big mess. So I decided to wait for the fix to come with FiJi's official updates, yet it still is not working. Am I doing something wrong? SCIFIO / BioFormats reports 4.5-dev in FiJi, all available updates are done...

With regard to updating to 4.4.7 with FiJi, these are the .jar files you need to delete:

jars/bio-formats-4.4.9-SNAPSHOT.jar
jars/jai_imageio-4.4.9-SNAPSHOT.jar
jars/loci-common-4.4.9-SNAPSHOT.jar
jars/mdbtools-java-4.4.9-SNAPSHOT.jar
jars/ome-xml-4.4.9-SNAPSHOT.jar
jars/poi-loci-4.4.9-SNAPSHOT.jar
jars/scifio-4.4.9-SNAPSHOT.jar
plugins/loci_plugins-4.4.9-SNAPSHOT.jar

Basically, everything ending with "-4.4.9-SNAPSHOT.jar". And then copy the 4.4.7 version of loci_tools.jar to

plugins/loci_tools.jar

As far as I understand, FiJi should be updated to use 4.4.7, but that's currently a work in progress, so not available just yet.

I hope this helps; please do let me know if you have any further trouble. The "4.5-dev" version should also include the slidebook support to the best of my knowledge; I'll double-check whether this is definitely the case.


Regards,
Roger Leigh

rleigh wrote:The "4.5-dev" version should also include the slidebook support to the best of my knowledge; I'll double-check whether this is definitely the case.

Support has been present since the 6th of March. I'm not sure how old the version currently in FiJi is.