How to switch between the 3 coordinate systems of Mouse Connectivity?

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How to transform CCF (x, y, z) coordinates into stereotactic coordinates

The Common Coordinate Framework (CCF) is defined in a basic image coordinate system, using the top-left-rear pixel as its origin, and incrementing in the X, Y and Z axes up to the number of pixels in each dimension (ML, DV, AP respectively). It was not designed as a targeting coordinate system. Using some transformations the CCF can be roughly aligned to the stereotactic atlas, however, since it was not it’s intended purpose one should take caution when using the CCF for targeting, even after ap…