I am not an intensive imageJ user, but in Fiji (which is basically an ImageJ), you have the "stacks" submenu in the image tab that allows you to render 3d (3D project).

And in the same fiji, you can also use plugins like "3D viewer" or "volume viewer" to get what you want from a stack.

Have fun

I am not an intensive imageJ user, but in Fiji (which is basically an ImageJ), you have the "stacks" submenu in the image tab that allows you to render 3d (3D project).

And in the same fiji, you can also use plugins like "3D viewer" or "volume viewer" to get what you want from a stack.

Have fun

Load your image into the 3D viewer (included with Fiji) Plugins > 3D Viewer. From the load window, you can choose display as Surface to generate 3D surface files. Once generated, export the surfaces from File>Export Surfaces the 3D surf file. If you only wish for a volume view, you may select that from the display.

There is a limited segmentation ability with the viewer. Entering a threshold in the load window will perform a simple intensity based threshold for Surface generation. It is much preferred to generate your own ideal segmentation and load this into the 3d viewer for surface generation.

Additionally, surface or volume rendering are visualization techniques that will facilitate your understanding (visually) of the 3D structure but are not useful for quantification. After reviewing your 3D structure, you may wish to use other methods to identify contact sites and quantify their prevalence, distribution, and localization.

Further elaboration of your analysis goals will help us to advise you better.

Thank you!!!

You may be interested in the information page for 3D viewer:

http://132.187.25.13/ij3d/?page=Screencasts&category=Documentation

If you have access to Imaris software, it provides very high quality 3D rendering for confocal images. Imaris also allows data analysis based on your 3D rendering parameters.