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What tools exist to derive geometries for use with modern GIS systems from older scanned maps? I am referring more to libraries that generate actual data rather than present an interface for manually editing or tracing features. If no such tools exist, are there any academic papers or research (or shameless hacks!) from related fields that might shed light on the problem?

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MapAnalyst - The Map Historian's Tool for the Analysis of Old Maps

Calculates Displacement in Historical Maps(displacement vectors,distortion grid,scale isolines,rotation isolines.)

"MapAnalyst is a Java application that runs on all major computer platforms. It allows for the efficient identification and management of control points in a historical map and in a corresponding reference map, and computes distortion grids, error vectors and isolines of scale and rotation. It offers a wide palette of parameters to fine-tune the generated graphics. MapAnalyst also computes the historical map’s scale, rotation angle and statistical indicators, and offers interactive tools to explore local variations of displacements, scale and rotation. MapAnalyst is freely available to all map historians, and its open-source code can be extended by anyone with Java programming skills. The software has been designed with a special focus on a user-friendly interface that allows historians without a technical background to easily analyze the geometry of old maps."

http://mapanalyst.cartography.ch/

Academic PDF on MapAnalyst http://jenny.cartography.ch/pdf/2007_Jenny_etal_MapAnalyst.pdf

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Oooh, I have to try that one sometime. –  relet Aug 23 '10 at 7:47
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The ESRI ArcGIS answer to the issue is ArcScan: "a comprehensive and easy-to-use set of tools for raster-to-vector conversion."

GRASS (open source) GIS possesses raster-to-vector conversion functionality: r.to.vect.

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