I'm running into an issue georeferencing a number of PNG image files. The files simply contain an image where each pixel is either transparent or a single color, forming a coverage mask. In the past, when I've georeferenced these images, the 'use 0 for transparency' checkbox masked off the transparent parts of the images and I was able to polygonize the colored parts. However, with a number of images in a recent patch QGIS will simply not mask off the transparent sections. I've opened the files with an image editor and resaved them to no effect, so it's not a formatting problem with the input png.
I can somewhat work around this by setting the value of the transparent section to the no data value, thus masking off the image in the raster layer. However, when I polygonize the raster, the no data value still gets polygonized into the .shp file.
How do I polygonize the raster and specify only the single band I want to polygonize?