Hi, there are a few ways you might do this: There's a Python library for command line use that can be run on image sequences or videos: https://github.com/publiclab/infrapix There's also this prototype I've been working on a bit which lets you drag an image into a sequence of processing steps, and it could be adapted for batch processing of NDVI as well, but it'd be a while before it's ready: https://github.com/jywarren/image-sequencer There's the Photo Monitoring Plugin for ImageJ, which is (i think) scriptable -- https://publiclab.org/wiki/photo-monitoring-plugin

I have used Ned's plugin for Fiji (https://publiclab.org/notes/nedhorning/01-13-2016/packaged-photo-monitoring-plugins-available-on-the-github-repositoy) to convert an NGB video into NDVI. See this note: https://publiclab.org/notes/cfastie/06-05-2013/bee-movie-ii. This will work for RGN videos too. Fiji allows videos to be opened as a stack of individual frames. Then the Photomonitoring plugin can convert each frame into NDVI and Fiji can output a video from the stack. Chris