Publications

2022

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

2021

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

Schütz, L M, Louveaux, M, Vilches-Barro, A, Bouziri, S, Cerrone, L, Wolny, A, Kreshuk, A, Hamprecht, F A and Maizel, A (2021). Integration of Cell Growth and Asymmetric Division during Lateral Root Initiation in Arabidopsis thaliana. Plant and Cell Physiology. 62 1269-1279

Pape, C, 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 (2021). Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera. BioEssays. 43

Roth, K, Milbich, T, Ommer, B, Cohen, J Paul and Ghassemi, M (2021). S2SD: Simultaneous Similarity-based Self-Distillation for Deep Metric Learning. Proceedings of International Conference on Machine Learning (ICML). https://arxiv.org/abs/2009.08348

Arlt, H, 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 (2021). Seipin forms a flexible cage at lipid droplet formation sites. bioRxiv

2020

Wolny, A, 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 (2020). Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution. eLife. 9

Milbich, T, Roth, K, Bharadhwaj, H, Sinha, S, Bengio, Y, Ommer, B and Cohen, J Paul (2020). DiVA: Diverse Visual Feature Aggregation for Deep Metric Learning. IEEE European Conference on Computer Vision (ECCV). https://arxiv.org/abs/2004.13458

Roth, K, Milbich, T, Sinha, S, Gupta, P, Ommer, B and Cohen, J Paul (2020). Revisiting Training Strategies and Generalization Performance in Deep Metric Learning. International Conference on Machine Learning (ICML). https://arxiv.org/pdf/2002.08473.pdf

Censor, Y, Petra, S and Schnörr, C (2020). Superiorization vs. Accelerated Convex Optimization: The Superiorized/Regularized Least Squares Case. J. Appl. Numer. Optimization (in press; arXiv:1911.05498). 2 15-62. http://jano.biemdas.com/archives/1060

2019

Jähne, (2019). Air-Sea Gas Exchange. Encyclopedia of Ocean Sciences. Academic Press. 6 1–13

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

Imle, A, 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 (2019). Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures. Nature Communications. 13;10(1)

Berg, S, 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 (2019). ilastik: interactive machine learning for (bio)image analysis. Nature Methods. 16 1226-1232

Censor, Y, Petra, S and Schnörr, C (2019). Superiorization vs. Accelerated Convex Optimization: The Superiorized/Regularized Least Squares Case. preprint: arXiv. https://arxiv.org/abs/1911.05498

2018

Cerrone, L (2018). Deep End-To-End Learning Of A Diffusion Process For Seeded Image Segmentation. Heidelberg University

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

2017

Beier, T, 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 (2017). Multicut brings automated neurite segmentation closer to human performance. Nature Methods. 14 101-102. http://rdcu.be/oVDQ

Ulman, V, 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 (2017). An Objective Comparison of Cell Tracking Algorithms. Nature Methods. 14 1141-1152

Technical Report (4.24 MB)

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

2016

Meijering, E, Carpenter, A E, Peng, H, Hamprecht, F A and Olivo-Marin, J (2016). Imagining the future of bioimage analysis. Nature Biotechnology. 34 1250-1255

Technical Report (924.57 KB)

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

2015

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

Mitra, N J, Stam, J, Xu, K, Cheng, M - M, Prisacariu, V Adrian, Zheng, S, Torr, P H S and Rother, C (2015). Pacific Graphics 2015 DenseCut: Densely Connected CRFs for Realtime GrabCut. 34. http://mftp.mmcheng.net/Papers/DenseCut.pdf

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

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

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

Technical Report (2.14 MB)

2014

Wahl, A - S, 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 (2014). Asynchronous Therapy Restores Motor Control by Rewiring of the Rat Corticospinal Tract after Stroke. Science. American Association for The Advancement of Science. 344 1250--1255. http://www.sciencemag.org/content/344/6189/1250

Zheng, S, Cheng, M Ming, Warrell, J, Sturgess, P, Vineet, V, Rother, C and Torr, P H S (2014). Dense semantic image segmentation with objects and attributes. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. 3214–3221. http://www.robots.ox.ac.uk/˜tvg/http://tu-dresden.de/inf/cvld

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

Technical Report (2.01 MB)

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

2013

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

Technical Report (2.13 MB)

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