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I have a raster file with no spatial reference. How can I define a projection for the image in ecognition software for classification purposes?

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I'm pretty certain that it's not possible with eCognition. You could try other software to define the coordinate system;

ArcGIS - "Define Coordinate System" tool

QGIS - If your raster file has no coordinate system, you will be prompted to select one. Then export the layer to a new file.

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