You can do that from File > Automate > Photomerge. There are various options you can play with.
After it's done you will have all images as layers with masks applied. You can select all of them and press Ctrl/Cmd + E to merge them into a single layer, or Right Click on them and Convert to smart object.
After you have a single layer, you have different selection options to choose from depending on the image, details, etc. You can use the Quick select tool, Object selection tool or from the menu Select > Color range if they are relatively uniform surfaces.
Once you've selected a patch you want to have as a separate image, you can right click on the selection and choose Layer Via Copy. Once that patch has been copied to a new layer, right click on that layer and choose Export As, to export it in whatever format you desire.
You also mentioned contours. Before you export the separated layer, with that layer selected, you can go to Layer > Layer Style > Stroke from the menu. There you can add a stroke / contour, playing with the options to get it to look how you want and hit Ok. If you only want the contours to be visible in the exported image, with the layer selected, reduce the Fill value to 0% in the layers panel, so only the applied stroke remains.
As you are new to Photoshop, I would dig in the Help and look up any terms mentioned so you better understand what's happening.
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