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I think everything in modules/js/src is not autogenerated. What it is autogenerated from those is build/modules/js/bindings.cpp I think that one is generated using the template and embindgen from modules/js/src and also which parts of the library goes there is defined in platforms/js/

I wonder exactly what's what you are trying to archive ? passing a Mat from JS to native function ? Did you consider wrapping existing cv.x javascript method with a custom js function that implement your magic ?