To make the process easier, the video frames are first converted to grayscale images, and then by applying a threshold they are converted to binary images.
Can I omit they or I should keep it?
To give the statement with utmost clarity, use 'they'. Something tells me that you're writing an instructional or report based document. This type of documentation should convey maximum information with least amount of ambiguity and confusion. Using 'they' will only give the sentence better clarity as to what you're "applying a threshold" to.