Hemispherical canopy photos

[Ariane5FDD]

I need to get all of the vegetation black and the all of the sky white (sometimes there are clouds in in the sky too. Can you see how the area with a red circle around them are still white once they have been thresholded? They need to be black as they will be misinterpreted as sky when I do the gap light analysis. 

I have been looking at the masking tool in Lightroom to paint all of the trees and ground before I threshold the image, but wondered if that is the correct way to do it. It still leaves some white spots in the sections I mask. I have been setting the exposure and black slider right down, but there are still white spots in the masked areas.