Extract ROI from image by hand into Matrix Form

Question

I have a 3D Image (each pixel contains information for various wavelengths). I draw the image for one wavelength by using

Image[img[[All, All, 100]]] // ImageAdjust

whereas img is my Image. Now I want to extract the Data in a certain ROI. I do so by using the mask tool, but when I copy the mask, I get a fullsize image where the selected mask is white (I selected the following three squares):

How to extract the information from img (fully including the wavelength-dimension) for these regions? I.e. discarding the black areas completely. ImageMultiply doesnt help me, as this would just make those areas black again and not really discarding them.

Thanks

Answer 1

I finally found a solution:

mask = (* As seen above, copied from masking tool as a "Image *)
pos = Position[mask // ImageData, 1];
spectra = Extract[img, pos];