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

[Kunis, Susanne]

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
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

The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________
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