Exporting from the 3D plugin

Posted by Matthew Jones on Aug 25, 2016; 11:02am
URL: http://imagej.273.s1.nabble.com/Exporting-from-the-3D-plugin-tp5017117.html

Hi,

Apologies if you recieve this twice, it came back blank to me the first time:

I am hoping to use the 3D plugin to study nuclear organisation. I am able to import my image, create a 3D projection using standard imageJ functions and then apply the imageJ 3D plugin to segment and binarise my nucleus nicely. However I am unable to figure out how to export this binary image after segmentation.

I’ve tried saving to various file formats but it seems that the 3D projection is not represented as a 3D array as I would expect.

Alternatively, converting the binary image back to a stack (in the original orientation) would be a very helpful intermediate step.

I tried saving as tif, but this is a tif of the 3D projection.

I also tried reslice, but this did not return a binary image stack as I had expected.

I’ve looked into using the TANGO plugin which looks ideal for my application, does anyone out there have a working knowledge of TANGO and would be able to answer a few questions about getting going with this?

Matt
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