Glad you are enjoying AGAVE.
We are definitely interested in getting your suggestions on how best to do this.
There is only one way to apply same settings to several files - this does need some improved user experience. Here is the way to do it for now:
Save to JSON.
The JSON is a text file. You can then make a copy of it, and replace the file path in the JSON file with the other stack.
One caveat is that the thresholding settings (window/level, percentile, isovalue, etc) are relative values and if your intensity ranges vary widely from one image to the next, the thresholding may not be perfectly consistent. I have an upcoming code change that tries to preserve absolute intensity levels across saves.
However, copying the JSON output should get you most of the way to using identical camera angle, lighting etc.
Then you can Load from JSON in the menus.
One thing I have considered is simply using a dialog box when you open a new image, so that you can have a checkbox for “preserve current settings”.