[ome-users] Viewer shows Zeiss SEM Auriga data as blank [5.2.4]

[Sebastien Besson (Staff)]

Dear Susanne,

You are right, the fix for this particular issue was carried out at the Bio-Formats level specifically
as part of this Pull Request [1] and was released together with Bio-Formats 5.2.0.

The fix unfortunately did not get backported to the 5.1.x line. However, looking at the diff it does
not seem to require any 5.2.0 specific feature. So it should be possible to integrate it into a local
development version of Bio-Formats.

Best,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/pull/2221

On 14 Sep 2016, at 12:44, Kunis, Susanne <Susanne.Kunis at Biologie.Uni-Osnabrueck.DE<mailto:Susanne.Kunis at Biologie.Uni-Osnabrueck.DE>> wrote:

Dear Mark,

thank you for your explanations, but the command-line access is not a solution for the users of our facility.

This is what i've try:
(I used ImageJ 1.50b)
# + Plugin Bio-Formats 5.1.8  load image file from local disc - works
# +Plugin Bio-Formats 5.1.8 Import from local disc - failed

# +Plugin Bio-Formats 5.2.2 load image from local disc - works
# +Plugin Bio-Formats 5.2.2 Remote Importer throws an exception:
java.lang.NegativeArraySizeException
at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:559)
at loci.formats.in.OMEXMLReader.isThisType(OMEXMLReader.java:100)
at loci.formats.FormatReader.isThisType(FormatReader.java:619)
at loci.formats.in.OMEXMLReader.isThisType(OMEXMLReader.java:111)
at loci.formats.ImageReader.getReader(ImageReader.java:181)

# +Plugin Bio-Formats 5.2.2 Import from local disc - works

The Remote Importer of Bio-Formats doesn't seem to access only the raw image on server? Or what ist the reason of this behaviour?

Do it understand it right, it is a problem of Bio-Formats? Maybe it could be a solution that i integrate the fixed code in my local Bio-Formats 5.1.8 , if the fix isn't so much invasiv...
I already looked for it at the GIT, but maybe you have a hint for me?

Cheers
Susanne

-----Ursprüngliche Nachricht-----
Von: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] Im Auftrag von Mark Carroll
Gesendet: Dienstag, 13. September 2016 14:25
An: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Betreff: Re: [ome-users] Viewer shows Zeiss SEM Auriga data as blank [5.2.4]

On 09/13/2016 01:16 PM, Mark Carroll wrote:

Easier and more likely to work is to use the Bio-Formats 5.2.2
command-line tools with the original file separately from OMERO.

Of course, I should have added that the 5.2.2 version of bioformats_package.jar also works just fine in ImageJ, I didn't mean to single out the command-line tools in particular so much as to say "separately from OMERO 5.2". You might still need to import the file into ImageJ from your local disk but /perhaps/ you could just use the plugin's "Bio-Formats Remote Importer" with your current server and see if it works directly too.

-- Mark

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