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

[Melissa Linkert]

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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