how to export stack aligned using TrakEM2 plugin?

[Bill Christens-Barry]

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

[Albert Cardona]

Hi Bill,


> 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).
>  


I would select the rectangle ROI, draw a ROI, then right-click and
choose Display - make flat image. Select the layer range, and a new
stack will be created.

Unfortunately I can't use ImageJ menu items (such as the "Save as ...")
because the current ij.CommandListener is very limited in scope. I have
created a new one, but it's not part of the standard ImageJ. More on
this soon.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona