Using a Surface to mask a channel in Imaris

1. Open you image in Imaris. In this example we have a neuron (red) in an image which also contains a marker found both inside and outside the cell (green spots)

2. Create a surface – see see how to create a surface if unsure.

3. Click on the newly created surface and under the Edit tab (the pencil) choose Mask All

5. In the window that appears choose the channel you wish to mask (here it is green) then, to clear all the spots inside the neuron we choose set voxels outside surface to 0. It is important to tick on the duplicate channel before applying Mask so that you don’t overwrite your original data.