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Conference Paper

Automatic alignment of stacks of filament data

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Dercksen, V., Weber, B., Gunther, D., Oberlaender, M., Prohaska, S., & Hege, H.-C. (2009). Automatic alignment of stacks of filament data. In 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (pp. 971-974). Piscataway, NJ, USA: IEEE.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0013-C3FD-8
We present a fast and robust method for the alignment of image stacks containing filamentous structures. Such stacks are usually obtained by physical sectioning a specimen, followed by an optical sectioning of each slice. For reconstruction, the filaments have to be traced and the sub-volumes aligned. Our algorithm takes traced filaments as input and matches their endpoints to find the optimal transform. We show that our method is able to quickly and accurately align sub-volumes containing neuronal processes, acquired using brightfield microscopy. Our method also makes it possible to align traced microtubuli, obtained from electron tomography data, which are extremely difficult to align manually.