I implement the collision detection in my project so I have for each object an origin and max and min vertices so I can calculate the collision detection simply not accurate which is I want at that stage, but I may have many instanced objects which is only one object and is repeated many times in the vertex shader using the transformation matrices I passed to it. I do the collision test in the CPU so it doesn't know anything about the instances except the matrix array of them. can I apply the method I use for instanced objects?
OpenGL collision detection with instanced object
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Of course, just transform your bounding box using each object's matrix, then apply collision detection to the transformed boxes.