### Currently we: - Use a coppafisher-specific tile indexing method. ### Issue: - It is confusing, especially with additional corrections like reversing the tile positions and rotating the tiles by 90 degrees anti-clockwise. ### Solution: - Use the exact same tile indexing as the inputted files, whatever input style they may be. - For nd2 files and JOBs files, this would come from the metadata inside the nd2 files. - For non-nd2 files, this would come from the tile positions specified in the given metadata.json file.
