[ome-users] problem when opening a .sdt file with loci-tools

[Melissa Linkert]

Hi Patrick,

Thank for sending the problematic .sdt file privately.

We now have a fix for the problem, as noted here:

https://github.com/melissalinkert/bioformats/commit/4d81baac2833063a92efb22c09ef827bd83b5641

A new build of Bio-Formats that contains this fix will be available in 1
to 2 weeks.

Regards,
-Melissa

On Thu, Apr 19, 2012 at 08:50:38AM -0400, Melissa Linkert wrote:
> Hi Patrick,
> 
> > I encounter the following problem when I want to open (by drag&drop, import or open) a .sdt file (Becker&Hickl SPC file - recorded with B&H SPCM version 9.42) with the loci_tools plugin for ImageJ: A window pops up with the correct number of pixels recorded but the value of all the pixels is equal to zero which results in an all black image.
> > I use ImageJ 1.45s and loci-tools 4.4 DEV (January 2012) / trunk build.
> > When I open the .sdt file using the B&H software it shows me the right data plot - so all the information about counts/pixel should be saved correctly within the .sdt file.
> > Do you have an idea how to get ImageJ/loci-tool to work with the .sdt file?
> 
> The first thing to do is to try using a more recent version of
> Bio-Formats - if you could please try installing the very latest trunk
> build of loci_tools.jar from:
> 
> http://loci.wisc.edu/bio-formats/downloads
> 
> and see if that works, that would be much appreciated (the build date
> should be 15 April 2012 or later).
> 
> If upgrading still does not solve the problem, then it would be very
> helpful if you could send the file in question.  If needed, I can
> provide you with SFTP server credentials for uploading the file in a
> private mail.
> 
> Regards,
> -Melissa
> 
> On Thu, Apr 19, 2012 at 09:20:11AM +0200, Schwab, Patrick wrote:
> > Hello,
> > 
> > I encounter the following problem when I want to open (by drag&drop, import or open) a .sdt file (Becker&Hickl SPC file - recorded with B&H SPCM version 9.42) with the loci_tools plugin for ImageJ: A window pops up with the correct number of pixels recorded but the value of all the pixels is equal to zero which results in an all black image.
> > I use ImageJ 1.45s and loci-tools 4.4 DEV (January 2012) / trunk build.
> > When I open the .sdt file using the B&H software it shows me the right data plot - so all the information about counts/pixel should be saved correctly within the .sdt file.
> > Do you have an idea how to get ImageJ/loci-tool to work with the .sdt file?
> > 
> > Thank you very much,
> > Patrick
> 
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>