Publications

2022

Q. Garrido, Damrich, S., Jäger, A., Cerletti, D., Claassen, M., Najman, L., and Hamprecht, F. A., “Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder”, Bioinformatics, vol. 38 (Suppl 1), pp. i316-i324, 2022.

2021

A. Vijayan, Tofanelli, R., Strauss, S., Cerrone, L., Wolny, A., Strohmeier, J., Kreshuk, A., Hamprecht, F. A., Smith, R. S., and Schneitz, K., “A Digital 3D Reference Atlas Reveals Cellular Growth Patterns Shaping the Arabidopsis Ovule”, eLife, 2021.

L. M. Schütz, Louveaux, M., Vilches-Barro, A., Bouziri, S., Cerrone, L., Wolny, A., Kreshuk, A., Hamprecht, F. A., and Maizel, A., “Integration of Cell Growth and Asymmetric Division during Lateral Root Initiation in Arabidopsis thaliana”, Plant and Cell Physiology, vol. 62, no. 8, pp. 1269-1279, 2021.

C. Pape, Remme, R., Wolny, A., Olberg, S., Wolf, S., Cerrone, L., Cortese, M., Klaus, S., Lucic, B., Ullrich, S., Anders-Össwein, M., Wolf, S., Cerikan, B., Neufeldt, C. J., Ganter, M., Schnitzler, P., Merle, U., Lusic, M., Boulant, S., Stanifer, M., Bartenschlager, R., Hamprecht, F. A., Kreshuk, A., Tischer, C., Kräusslich, H. - G., Müller, B., and Laketa, V., “Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera”, BioEssays, vol. 43, no. 3, 2021.

K. Roth, Milbich, T., Ommer, B., Cohen, J. Paul, and Ghassemi, M., “S2SD: Simultaneous Similarity-based Self-Distillation for Deep Metric Learning”, Proceedings of International Conference on Machine Learning (ICML). 2021.

H. Arlt, Sui, X., Folger, B., Adams, C., Chen, X., Remme, R., Hamprecht, F. A., DiMaio, F., Liao, M., Goodman, J. M., Farese, R. V., and Walther, T. C., “Seipin forms a flexible cage at lipid droplet formation sites”. bioRxiv, 2021.

2020

A. Wolny, Cerrone, L., Vijayan, A., Tofanelli, R., Vilches-Barro, A., Louveaux, M., Wenzel, C., Strauss, S., Wilson-Sanchez, D., Lymbouridou, R., Steigleder, S. S., Pape, C., Bailoni, A., Duran-Nebreda, S., Bassel, G. W., Lohmann, J. U., Tsiantis, M., Hamprecht, F. A., Schneitz, K., Maizel, A., and Kreshuk, A., “Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution”, eLife, vol. 9, 2020.

T. Milbich, Roth, K., Bharadhwaj, H., Sinha, S., Bengio, Y., Ommer, B., and Cohen, J. Paul, “DiVA: Diverse Visual Feature Aggregation for Deep Metric Learning”, IEEE European Conference on Computer Vision (ECCV). 2020.

K. Roth, Milbich, T., Sinha, S., Gupta, P., Ommer, B., and Cohen, J. Paul, “Revisiting Training Strategies and Generalization Performance in Deep Metric Learning”, International Conference on Machine Learning (ICML). 2020.

Y. Censor, Petra, S., and Schnörr, C., “Superiorization vs. Accelerated Convex Optimization: The Superiorized/Regularized Least Squares Case”, J. Appl. Numer. Optimization (in press; arXiv:1911.05498), vol. 2, pp. 15-62, 2020.

2019

B. Jähne, “Air-Sea Gas Exchange”, Encyclopedia of Ocean Sciences, vol. 6. Academic Press, pp. 1–13, 2019.

L. Cerrone, Zeilmann, A., and Hamprecht, F. A., “End-to-End Learned Random Walker for Seeded Image Segmentation”, CVPR. Proceedings. pp. 12559-12568, 2019.

A. Imle, Kumberger, P., Schnellbächer, N. D., Fehr, J., Carillo-Bustamente, P., Ales, J., Schmidt, P., Ritter, C., Godinez, W. J., Müller, B., Rohr, K., Hamprecht, F. A., Schwarz, U. S., Graw, F., and Fackler, O. T., “Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures”, Nature Communications, vol. 13;10(1), 2019.

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.

Y. Censor, Petra, S., and Schnörr, C., “Superiorization vs. Accelerated Convex Optimization: The Superiorized/Regularized Least Squares Case”, preprint: arXiv, 2019.

2018

L. Cerrone, “Deep End-to-End Learning of a Diffusion Process for Seeded Image Segmentation”, Heidelberg University, 2018.

N. Rahaman, Arpit, D., Baratin, A., Draxler, F., Lin, M., Hamprecht, F. A., Bengio, Y., and Courville, A., “On the spectral bias of deep neural networks”, arXiv preprint arXiv:1806.08734, 2018.

2017

T. Beier, Pape, C., Rahaman, N., Prange, T., Berg, S., Bock, D., Cardona, A., Knott, G. W., Plaza, S. M., Scheffer, L. K., Köthe, U., Kreshuk, A., and Hamprecht, F. A., “Multicut brings automated neurite segmentation closer to human performance”, Nature Methods, vol. 14, no. 2, pp. 101-102, 2017.

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)

S. Peter, Kirschbaum, E., Both, M., Campbell, L. A., Harvey, B. K., Heins, C., Durstewitz, D., Diego, F., and Hamprecht, F. A., “Sparse convolutional coding for neuronal assembly detection”, NIPS, poster. 2017.

2016

E. Meijering, Carpenter, A. E., Peng, H., Hamprecht, F. A., and Olivo-Marin, J., “Imagining the future of bioimage analysis”, Nature Biotechnology, vol. 34, no. 12, pp. 1250-1255, 2016.

Technical Report (924.57 KB)

Y. Censor, Gibali, A., Lenzen, F., and Schnörr, C., “The Implicit Convex Feasibility Problem and Its Application to Adaptive Image Denoising”, J. Comp. Math., vol. 34, pp. 608-623, 2016.

2015

S. Zheng, Prisacariu, V. Adrian, Averkiou, M., Cheng, M. Ming, Mitra, N. J., Shotton, J., Torr, P. H. S., and Rother, C., “Object proposals estimation in depth image using compact 3D shape manifolds”, in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2015, vol. 9358, pp. 196–208.

N. J. Mitra, Stam, J., Xu, K., Cheng, M. - M., Prisacariu, V. Adrian, Zheng, S., Torr, P. H. S., and Rother, C., “Pacific Graphics 2015 DenseCut: Densely Connected CRFs for Realtime GrabCut”, vol. 34, 2015.

C. Cali, Baghabra, J., Boges, D. J., Holst, G. R., Kreshuk, A., Hamprecht, F. A., Srinivasan, M., Lehväslaiho, H., and Magistretti, P. J., “Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues”, Journal of Comparative Neurology, vol. 524, pp. 23-38, 2015.

D. Kiefhaber, Caulliez, G., Zappa, C. J., Schaper, J., and Jähne, B., “Water wave measurement from stereo images of specular reflections”, vol. 26, p. 115401, 2015.

A. Kreshuk, Funke, J., Cardona, A., and Hamprecht, F. A., “Who is talking to whom: synaptic partner detection in anisotropic volumes of insect brain”, MICCAI. Proceedings, vol. LNCS 9349. Springer, pp. 661-668, 2015.

Technical Report (2.14 MB)

2014

A. - S. Wahl, Omlor, W., Rubio, J. C., Chen, J. L., Zheng, H., Schröter, A., Gullo, M., Weinmann, O., Kobayashi, K., Helmchen, F., Ommer, B., and Schwab, M. E., “Asynchronous Therapy Restores Motor Control by Rewiring of the Rat Corticospinal Tract after Stroke”, Science, vol. 344, p. 1250--1255, 2014.

S. Zheng, Cheng, M. Ming, Warrell, J., Sturgess, P., Vineet, V., Rother, C., and Torr, P. H. S., “Dense semantic image segmentation with objects and attributes”, in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2014, pp. 3214–3221.

B. Maco, Cantoni, M., Holtmaat, A., Kreshuk, A., Hamprecht, F. A., and Knott, G. W., “Semiautomated Correlative 3D Electron Microscopy of In Vivo Imaged Axons and Dendrites”, Nature Protocols, vol. 9, pp. 1354-1366, 2014.

Technical Report (2.01 MB)

B. Goldlücke, Aubry, M., Kolev, K., and Cremers, D., “A super-resolution framework for high-accuracy multiview reconstruction”, Int. J. Comp. Vision, vol. 106, p. 172--191, 2014.

2013

B. Maco, Holtmaat, A., Cantoni, M., Kreshuk, A., Straehle, C. N., Hamprecht, F. A., and Knott, G. W., “Correlative in vivo 2 photon and focused ion beam scanning electron microscopy of cortical neurons”, PloS one, vol. 8 (2), 2013.

Technical Report (2.13 MB)

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