There should be an option to add a Save Overlay button which should allow you to grab the overlay specifically. As to your second question: I think you can send data either to a file, or to a buffer which can be read out using `skimage.io.pop`. I've used this before, but my memory is a bit fuzzy on it now. If this isn't currently available for scripting like your hoped-for functionality example, I'm sure it could be implemented.

Thanks for the PR fixing the save dialog if it's RGB!

On Monday, October 28, 2013 2:19:03 AM UTC-5, Juan Nunez-Iglesias wrote:

Hi all, but especially @tonysyu:

I'm using the viewer for the first time to add some interactivity to my work. Please forgive the noobish-ness: I've only ever worked on command-line stuff. (Thanks btw to @tonysyu for his awesome SciPy lightning talk, which inspired me to even dip my toes in this!)

I'm running an RGB image through a bunch of thresholding and morphological operations, and I want to fiddle with the parameters before getting back the filter output. I'm running into the following problems:

1) The file > save as dialog saves a composite image of the overlay and underlying image, where I just want the overlay.

2) The file > save as dialog actually crashes when the underlying image is RGB! (PR forthcoming)

3) But most of all, I don't actually want to save the overlay, I just want to return it to the calling process. How would one go about this? Here's my code now:

v = viewer.ImageViewer(rgbs[0])
v += CentroPlugin()
v.show()

which works as expected. I'd like something like:

v = viewer.ImageViewer(rgbs[0])
v += CentroPlugin()
overlay = v.show()

Is this possible?

Thanks,

Juan.