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Book Chapter

C. Haubold, Schiegg, M., Kreshuk, A., Berg, S., Köthe, U., and Hamprecht, F. A., “Segmenting and Tracking Multiple Dividing Targets Using ilastik”, in Focus on Bio-Image Informatics, vol. 219, Springer, 2016, pp. 199-229.

Technical Report (4.46 MB)

Conference Paper

M. Schiegg, Heuer, B., Haubold, C., Wolf, S., Köthe, U., and Hamprecht, F. A., “Proof-reading Guidance in Cell Tracking by Sampling from Tracking-by-assignment Models”, in ISBI. Proceedings, 2015, pp. 394-398.

Technical Report (648.55 KB)

A. Drory, Haubold, C., Avidan, S., and Hamprecht, F. A., “Semi-Global Matching: A Principled Derivation in Terms of Message Passing”, in GCPR. Proceedings, 2014, pp. 43-53.

Technical Report (2.6 MB)

Conference Proceedings

C. Haubold, Uhlmann, V., Unser, M., and Hamprecht, F. A., “Diverse M-best Solutions by Dynamic Programming”, GCPR. Proceedings, vol. LNCS 10496. Springer, pp. 255-267, 2017.

C. Haubold, Ales, J., Wolf, S., and Hamprecht, F. A., “A Generalized Successive Shortest Paths Solver for Tracking Dividing Targets”, ECCV. Proceedings, vol. LNCS 9911. Springer, pp. 566-582, 2016.

Technical Report (1.18 MB)

Journal Article

V. Uhlmann, Haubold, C., Hamprecht, F. A., and Unser, M., “Diverse Shortest Paths for Bioimage Analysis”, Bioinformatics, pp. 1-3, 2017.

M. Schiegg, Hanslovsky, P., Haubold, C., Köthe, U., Hufnagel, L., and Hamprecht, F. A., “Graphical Model for Joint Segmentation and Tracking of Multiple Dividing Cell”, Bioinformatics, vol. 31, no. 6, pp. 948-956, 2015.

Technical Report (534.29 KB)

S. Berg, Kutra, D., Kroeger, T., Straehle, C. N., Kausler, B. X., Haubold, C., Schiegg, M., Ales, J., Beier, T., Rudy, M., Eren, K., Cervantes, J. I., Xu, B., Beuttenmüller, F., Wolny, A., Zhang, C., Köthe, U., Hamprecht, F. A., and Kreshuk, A., “ilastik: interactive machine learning for (bio)image analysis”, Nature Methods, vol. 16, pp. 1226-1232, 2019.

V. Ulman, Maška, M., Magnusson, K. E. G., Ronneberger, O., Haubold, C., Harder, N., Matula, P., Matula, P., Svoboda, D., Radojevic, M., Smal, I., Rohr, K., Jaldén, J., Blau, H. M., Dzyubachyk, O., Lelieveldt, B., Xiao, P., Li, Y., Cho, S. - Y., Dufour, A., Olivo-Marin, J. C., Reyes-Aldasoro, C. C., Solis-Lemus, J. A., Bensch, R., Brox, T., Stegmaier, J., Mikut, R., Wolf, S., Hamprecht, F. A., Esteves, T., Quelhas, P., Demirel, Ö., Malström, L., Jug, F., Tomančák, P., Meijering, E., Muñoz-Barrutia, A., Kozubek, M., and Ortiz-de-Solorzano, C., “An Objective Comparison of Cell Tracking Algorithms”, Nature Methods, vol. 14, no. 12, pp. 1141-1152, 2017.

Technical Report (4.24 MB)

PhD Thesis

C. Haubold, “Scalable Inference for Multi-Target Tracking on Proliferating Cells”. University of Heidelberg, 2017.