Bio-Format import of .vsi file?

Posted by Kenneth R Sloan on May 29, 2015; 6:56pm
URL: http://imagej.273.s1.nabble.com/Bio-Format-import-of-vsi-file-tp5012986.html

I have a Java plugin that reads .vsi files using the Bio-Format importer:

  //run Bio-Formats Importer on that file, taking the defaults
        IJ.run("Bio-Formats Importer", "open=" + dir + filename
               + " autoscale color_mode=Custom view=Hyperstack stack_order=XYCZT"
               + " series_1 series_0_channel_0_red=0 series_0_channel_0_green=255"
               + " series_0_channel_0_blue=0");


I believe that this worked recently (within the last 6 months) but now fails (note: I’m not completely sure of this behavior on exactly the same file - I’m working on that).

The current behaviour is that there is a Stack with exactly 3 images.  Two are identical, and look like like a reasonable single slice (in Green).  The third and last slice in the stack is solid BLACK.

Help, please!

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Kenneth Sloan
[hidden email]<mailto:[hidden email]>
Vision is the art of seeing what is invisible to others.





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