Re: how to export stack aligned using TrakEM2 plugin?

Posted by Albert Cardona on May 01, 2008; 9:36pm
URL: http://imagej.273.s1.nabble.com/how-to-export-stack-aligned-using-TrakEM2-plugin-tp3696365p3696366.html

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