First thing to do is to separate the left and right images. That's easy enough to do in Gimp using the "Rectangle Select" tool.
Once you have the left and right chips, they can be loaded into StereoPhoto Maker (SPM) and this is where the magic should happen. First thing to do is to align the two images using "adjust->auto alignment". Make sure that you have selected " Better Precision (Slow)" in "Edit->Preferences" (tab: Adjust) prior. It's time to generate the depth map by clicking on "Edit->Depth Map->Create depth map from stereo pair". Do not click on "Get values automatic" to get the background and foreground values, use the arrow keys. Do not let SPM resize your images by making sure your image size is smaller than the "maximum image width" (default = 3000). If unsure, just put a super large number in the box for "maximum image width". If your image size is about 1,000 pixels in width, the default values should be good except maybe the radius for DMAG5 which can be changed from 16 to 32.
The depth map you get should be ok but most likely far from being perfect. Click on "Edit->Depth Map->Correct depth map" to access the very useful depth map correction tool. It's very simple to use. Keep "Ctrl" pressed and use right-click to select a color in the depth map and left-click to paint the depth map.
To get rid of outliers, you may want to go into Gimp and use Filters->Blur->Median Blur. You can also use Filters->Blur->Selective Gaussian Blur to smooth the depth map without losing too much definition.
Here's a video that shows how I get a proper depth map in SPM from a scanned stereo slide:
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