When graphing 3d data, it is often clearer to use a color map than to plot a surface in three dimensions. Use a clear color scale with an obvious mapping. This will make it easier to read. See 3-Dim Plot with a Color-Map (pm3d) for examples.
To plot something like this:
you can use these commands:
set terminal png size 600,600 crop # output a 600x600 pixel png image set pm3d map # use 3d color map plot set xrange [1:321] # manually set range of x-axis set yrange [1:321] set size square # make the plot square unset key # don't show key set format x '' # don't show axis label set format y '' set cbrange [0:25] # the range of the z data set output 'out.png' # the output file name set title 'the title' # graph title splot 'data.out' using 1:2:3 # plot the data file using the first three columns