How to use "3DRoiManage"r?

Being a relative newbie, I need some help with the plugin “3DRoiManager”. Can someone direct me to a website or briefly explain here how to use this tool? I downloaded it, unzipped into my plugins, and restarted ImageJ (updated to latest version). But don’t know what to do next. I can’t find a plugin named “3DRoiManager”, let alone use it! And yes, I have read the tutorial ( However, that tutorial already assumes a higher level of expertise. I need some help from square one: where do I locate 3DRoiManager, how do I open a .tif image such as:
using 3DRoiManager, etc.

Any guidance would be greatly appreciated!

Hi @sroper,

first of all, you probably need to install the plugin of the 3D Roi Manager. To get it running in your FIJI installation, just enable the “3D ImageJ Suite” update site like explained here:

You will then find in the menu Plugins > 3D > 3D Roi manager.

However, the example you were showing is not a 3D data set and will probably not well work in the 3D Roi manager. It obviously has just two dimensions. We could guide you a bit better in the world of ImageJ/FIJI, if you tell us a bit more about the analysis you would like to do.


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Thanks so much for your reply, Robert!

Here is what I am doing: I am
conducting calcium imaging on a neural network. I collect a stack of images
from an x,y,t scan (N~500) that shows me the location and time that a neuron
becomes active. I then draw an Roi over the neuron, fill all the Roi’s with
black, fill the image of the neurons with white, and collapse the stack to a
single slice so that I can see where all the activated neurons are located (time
element is lost, obviously). I get images showing a distribution of black ovals/circles over a white background in a single .tif image (as shown in my original post). There is no longer any 3rd dimension, I recognize.

Here is my goal: I want to find if there are clusters of neurons (closely spaced groups of 2 or more Rois’s) that might suggest cell-cell interactions. I treat the neural assembly with different drugs that might create or abolish cell-cell interactions, and thus would change clustering. I would like to quantify this change in clustering, if it occurs.

Do you have any suggestions on how to approach my problem?

thanks for your help. I deeply appreciate this assistance!

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