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In a 3rd generation CT system, a single source projects the entire held of view (FOV) onto a large detector opposite the source. In multi-source CT imaging, a multitude of sources sequentially project a part of the FOV on a much smaller detector. These sources may be distributed in both the trans-axial and axial directions in order to jointly cover the entire FOV. For a full scan case, scan data from multiple sources in the axial direction provide complementary information. We previously proposed window-based 3D analytic cone-beam reconstruction and showed that multi-source CT can extend the axial scan coverage to 100mm without cone-beam artifacts. However for less than a full scan case, conjugate rays are not available most of time. We propose a cone-angle dependent weighting approach to combine multi-source data from less than full scan. We compute the amount of contribution from each longitudinal source to the each voxel by considering the X-ray beam collimation, the cone-angle from each source and the geometrical relationship between sources. The proposed techniques successfully reduce artifacts as illustrated by the experiments.