I’m not sure where the origin of the coordinates for the submission file should be.
I understand from the overview of the challenge that the bottom must be z = 0 and the top z = 1249.
From my understanding, it is the opposite of the numpy coordinates, isn’t it? See figure below:

So, is the origin of the coordinate system for the submission file therefore the lower, front, left corner of the numpy array describing the environment?

There is some confusion here. Z index 0 is the top, Z index 1250 is the bottom. Double-check this by plotting the data. The top of the model is effectively the surface of the ocean, jut like seismic data used in the geosciences.

To be clear, the coordinates we’re discussing are the indexes for the numpy array. You are correct; there is no index 1250. It would be index 1249. The values in the array are either 0 (no accumulation) or 1 (accumulation present). A submission file should provide the numpy array indexes of the 1’s, where the agents are or where they died.