Posted by
Thomas Boudier-4 on
Aug 26, 2016; 12:32am
URL: http://imagej.273.s1.nabble.com/Exporting-from-the-3D-plugin-tp5017117p5017123.html
Hi Matt,
By 3D Plugin, are you referring to the "3D Suite" ? Because there are
many 3D plugins for ImageJ/Fiji ;) .
http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:startAfter binarisation, just save your segmented nucleus as a tif file, tiff
formant can handle 3D . Actually I do not understand what you want to do ?
TANGO can be a nice tool for you to use, along with NucleusJ :
http://biophysique.mnhn.fr/tango/abouthttp://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:startPlease do not hesitate if you have more questions or comments.
Best,
Thomas
On 25/08/2016 19:02, Matthew Jones wrote:
> 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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>
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Thomas Boudier, Associate Professor, UPMC,
Université Pierre et Marie Curie, Paris, France.
BioInformatics Institute (BII)/IPAL, Singapore.
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