Exporting from the 3D plugin

[Matthew Jones]

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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[Thomas Boudier-4]

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:start

After 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/about

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start

Please 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
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
  /***************************************************************/
       Thomas Boudier, Associate Professor, UPMC,
       Université Pierre et Marie Curie, Paris, France.
       BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

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