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I would like to see additional input tools for common raster formats such as .BIL, .IMG, etc. Functionality similar to the inputs for MapInfo Vertical mapper .grc and .grd (which are not very common) would be great, but an added feature would be to provide an option to load the data as centroids or centroid lat/longs only. I have found that aligning multiple grc/grd layers based on centroid lat/long allows for cross-file analysis that is much more intuitive than other methods (i.e. R or ESRI), but it takes significant time to parse individual boxes and then calculate the centroid as a second step.
A super added bonus would be the ability to output raster files.