I have a merged image stack (from two composite stacks), with a screenshot of a slice shown here. This was done in ImageJ. Essentially, the water (blue) was injected into a gas diffusion layer (i.e., a porous material made primarily of carbon fiber). The black regions are air. How can I take that merged stack and create a new image stack of only the black region in ImageJ?
To put things in context, I'm eventually going to take the three different stacks (gas diffusion layer, water, air), create meshes from them, and find where the three all intersect (i.e., the triple-phase contact line). After some smoothing, I'll then calculate vertex normals along all the contact lines to calculate average contact angles of water in the gas diffusion layer.
So turns out my issue was how I combined the two images in the first place. Originally I used the Image > Color > Merge Channels option. But it was the fact that the merged stack now had two colors (not including the black background that I was trying to extract).
I took the two original stacks (water and GDL) and made them black and white. I then used the Process > Image Calculator feature to add the two stacks. I processed all the images.
Because I wanted the air (i.e. the background) I inverted the stack so that the air became white and the GDL and water became black. Then I was able to save this stack and eventually create a .stl file via ImageJ's 3D Viewer plugin (Plugins > 3D Viewer).