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Can I give small subsets of images as training areas in deep learning?

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I am working on forest tree species classification problem using CNN. I am working on UAV images. Instead of using entire images for training, I want to give several smaller subsets (like the training area polygons which is generally used in other supervised classification methods) as a training set. This is because a single UAV image has several different types of trees which have to be classified. Is this possible?

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