Exporting from the 3D plugin

[Matthew Jones]

Hi,

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?

I’ve attached an example image and a tif of the binarised and segmented blue channel which is in the undesired 3D projection format. I’d like to convert this to a standard z stack if possible.

Matt


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