To use this plugin, you have to use a 3 dimensional image (Third dimension being either Z or T). You can select the sequence to work on through the plugin's interface, and you then have to confirm it.
Once the sequence is confirmed, the plugin will open to viewers : one Orthogonal view where the work will be done, and one 3D one used to visualize your image. These viewers are linked, closing one will result in closing the other one.
You can navigate in your image with the Orthogonal view as usual, once you are on a point of interest, you can use the check box "lock" to stay in the current position and start delimiting the points that will generate the ellipsoid. You can do that either by clicking, which will result on a point, or by holding the MAJ key and moving the mouse (for a more approximate delimitation). Right-clicking will cancel the last added point.
You can use the crosshair to define your Region of Interest in every plane of the view. After that, you can either unlock the view to delimitate another region (the first one will be stored), or start the plugin to generate the ellipsoid.
The checkbox "display points" will add the clicked points in the 3D view, if you add points while the option is selected, they will also be displayed as sphere with radius 1 pixel.
You can also save created ellipsoid as XML files to later rebuild them in another image.
Selecting one ellipsoid in the "Layers" page of Icy will allow you to change name and/or color to help you recognise the different ellipsoids.
The method Ellipses is a work in progress and can't currently be used