how to export stack aligned using TrakEM2 plugin?

Posted by Bill Christens-Barry on May 01, 2008; 5:07pm
URL: http://imagej.273.s1.nabble.com/how-to-export-stack-aligned-using-TrakEM2-plugin-tp3696365.html

I've been using the TrakEM2 plugin to align a z-stack of hyperspectral images. It calculates the
alignment quite nicely and displays an aligned stack within the plugin project windows, but I'm
unsure about how I can export the aligned stack simply as a TIFF stack (I'm not interested in other
project files that obtain).

When I try the project export procedure given in the manual (v0.4y, 2007-12-19), no new TIFF is
saved up and I get an error dialog that says:

  Duplicate keyword:

    Command: "Tiff..."
    Keyword: "save"
    Value [/SomePath]

  Add an underscore to the corresponding label
  in the dialog to make the first word unique.

A .dtd file is created, but no TIFF.

Alternatively, if, after having TrakEM2 do the alignment, I try to save the aligned stack using the
File>SaveAs... menu item, I get an error:

java.lang.IndexOutOfBoundsException
        at java.io.FileOutputStream.writeBytes(Native Method)
        at java.io.FileOutputStream.write(FileOutputStream.java:260)
        at java.io.BufferedOutputStream.write(BufferedOutputStream.java:105)
        at java.io.DataOutputStream.write(DataOutputStream.java:90)
        at ij.io.ImageWriter.write8BitImage(ImageWriter.java:28)
        at ij.io.ImageWriter.write(ImageWriter.java:201)
        at ij.io.TiffEncoder.write(TiffEncoder.java:117)
        at ij.io.FileSaver.saveAsTiff(FileSaver.java:90)
        at ij.io.FileSaver.saveAsTiff(FileSaver.java:71)
        at ij.plugin.filter.Writer.run(Writer.java:20)
        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:243)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)
        at ij.IJ.runPlugIn(IJ.java:133)
        at ij.Executer.runCommand(Executer.java:104)
        at ij.Executer.run(Executer.java:55)
        at java.lang.Thread.run(Thread.java:613)


All of this on Mac OS 10.5.2 Intel-Mac. Does anyone have suggestions?

Thanks.

Bill Christens-Barry