Now that you have the data, what to do with it? Read my book, Beginning Python Visualization (2nd edition).  See http://www.apress.com/9781484200537 or click on Help|Beginning Python Visualiztion in the menu bar.
Right-clicking with the mouse on an already selected patch, deselects it
To select several patches at once, left click on an empty area to start a selection rectangle and drag it with the left mouse button pressed to include all the patches at once
You can use the mouse scroll wheel to zoom in and out
You can change the area to process by creating a new process area; this is done by pressing the CTRL button while left clicking the mouse button and creating a selection area rectangle
You can paste an image directly to im2graph (CTRL V)
To optimally set the viewing area, press CTRL and '+'
To convert logarithmic graphs, use the logarithmic scale option from the Options dialog box
If a graph isn't selected, try lowering the threshold value
If the graph and the grid are connected, try using degrid: horizontal, vertical or both.
Selected patches are marked in magenta
If you do not set the scales, default values will be used- each pixel equivalent to one unit
You can view the cursor location in im2graph's status bar
If it's hard to distinguish between the detected patches and the original graph colors, set the option "Show Results on White Background" available from the Options dialog
You can set the minimum patch size from the Options dialog
To undo all selections, click the Revert button
To zoom around a specific area, place the mouse over the area to zoom and zoom using the mouse scroll wheel
You can de-select several patches at once by mouse-right clicking and dragging a de-selection frame (blue thin frame)
