Enlarge or redraw 3D ROIs

3d
roi
Tags: #<Tag:0x00007fb88293ed28> #<Tag:0x00007fb88293ea58>

#1

Dear all,

Is there an easy way to enlarge or re-draw the 3D ROIs generated by the 3D Segmentation from the 3D ImageJ Suite?
I am segmenting nuclei and would like to make all the final ROIs spheres of a manually specified radius.

Thank you in advance for the help.

Rafael


#2

Hi @Buono,

If you want to enlarge the volumes of the objects, you may want to dilate the segmented image, you can use the filter 3D maximum to do this.

If you want to draw a sphere with a given radius at a given postilion you can use 3D draw shape from the 3D suite.

Regarding nuclei segmentation and analysis, you may want to have a look to TANGO or http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start.

Best,

Thomas


#3

Hi @ThomasBoudier,

Thank you for answering so fast!
I also ended finding this answer from you in another topic.
Using the 3D maximum seems to do the trick, but it is very very slow.

With the 3D Maxima Finder I could find all my nuclei. I was hoping to use that information to simply redraw all of them as spheres of a defined radius. If I try to use 3D draw shape it seems that I would have to enter the info one by one. I was hoping for an automated way to simply redefine all the ROIs into the spheres (read: a couple of buttons to click). I couldn’t find that. Is there a way? Maybe a macro alternative for feeding the ROIs obtained from 3D Maxima Finder into the 3D draw shape?

As for the nuclei segmentation solutions you mentioned, they might be a bit overkill for my current application. At this point I am not really interested in nuclear architecture. I just have quite round nuclei with nuclear localized red and green fluorescent proteins on them, and just want to know how much of red and how much of green I have. I am also interested in having object based colocalization done on the red and green. Essentially trying to answer: how many of my nuclei are both red and green, does presence of green always lead to absence of red.

Once again, thank you for the help.

Rafael


#4

Hi @Buono,

Here a simple macro that will do the job. Open the labelled image and run the macro. You can adjust the radius of the sphere inside the macro. You can find the macro on the 3D Manager page.

Hope this helps.

Best,

Thomas