I've never used FFMPEG for image sequences before but it occurs to me it could be an efficient means in future.

It may be necessary however to initially figure out a number pixels by which to offset the output frame in case important details are happening in the top or the bottom are lost in the output, that's something I'd need to know how to do too but to start with I'll assume we can just lop off the top and bottom equally. For simplicity's sake I would initially try do this by simply cropping an equal amount of pixels from both the top and bottom of each frame essentially leaving us with an image only of the middle portion of each image in a 16:9 ratio. Given the different aspect ratios and frame sizes, of the input from the output, I would expect it would be necessary to crop the the input images during the process of creating the video file as that would be preferable to distorting the images to fit a different aspect ratio. I have thousands of sequentially named JPEG images for use in creating a timelapse for HD video.

Ffmpeg crop video picture