[ome-users] fiji bug report - space in name

[fujisaws at mskcc.org]

I have a similar experience with Bio-Formats Export as Patrick (see below). It bugs out and doesn't export anything.



But I figured out that if the file name had a space, it doesn't export. The function works fine if there's no space in the name. So I wrote a macro to create a name without any spaces, and I was able to export all my images.



Hope this helps.


Sho Fujisawa
Sr. Digital Microscopist
Molecular Cytology Core Facility
Memorial Sloan-Kettering Cancer Center
417 E. 68th St.
Zuckerman Room 1834
New York NY 10065
(212) 639-6667
(646) 888-2186






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Hi Patrick,



You might be able to obtain more information about what's going wrong using the "debugging JVM hangs" instructions [1] on the ImageJ web site.



You could also try with a different version of Java [2, 3] and see if that makes a difference.



Regards,

Curtis



[1] http://imagej.net/Debugging#Debugging_JVM_hangs

[2]

http://imagej.net/FAQ#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F

[3] http://imagej.net/FAQ#How_do_I_set_up_Java_6_on_OS_X.3F





On Thu, Jul 30, 2015 at 6:44 AM, Patrick Weber <mail.pweber at gmail.com<mailto:mail.pweber at gmail.com>>

wrote:



> Dear all,

>

> I encountered a problem using the Bio-Formats exporter today. Every

> time I want to use it to export opened and processed (and even

> un-processed) OME.TIFF files, Fiji crashes, i.e. it shows Bio-formats

> exporter in the main window but stops working...

>

> I already rebooted, restarted Fiji several times, updated to an

> earlier version of Fiji/ImageJ but none of it worked... There is also

> no error message or something.

>

> Version Information:

>

> Fiji - Version 1.50a

> Java - 1.8.0_51 (64-bit)

> Mac OS X Yosemite 10.10.3

>

> I attached a screenshot showing the process after I chose the exporter

> plugin. As I mentioned there is no error message or something, but I

> even have to quit Fiji using the activity monitor.

>

> Hope you can help me with this. Thanks a lot!

>

> Patrick

>


Sho Fujisawa
Sr. Digital Microscopist
Molecular Cytology Core Facility
Memorial Sloan-Kettering Cancer Center
417 E. 68th St.
Zuckerman Room 1834
New York NY 10065
(212) 639-6667
(646) 888-2186


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