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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
Andersson, A, Diego, F, Hamprecht, F A and Wählby, C (2021). Istdeco: In Situ Transcriptomics Decoding By Deconvolution. bioRxiv
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
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
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
Walter, F C, Damrich, S and Hamprecht, F A (2021). MultiStar: Instance Segmentation of Overlapping Objects with Star-Convex Polygons. ISBI. 295-298PDF icon Technical Report (1.83 MB)
Kotovenko, D, Wright, M, Heimbrecht, A and Ommer, B (2021). Rethinking Style Transfer: From Pixels to Parameterized Brushstrokes. Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR). https://compvis.github.io/brushstroke-parameterized-style-transfer/
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
Brattoli, B, Büchler, U, Dorkenwald, M, Reiser, P, Filli, L, Helmchen, F, Wahl, A - S and Ommer, B (2021). Unsupervised behaviour analysis and magnification (uBAM) using deep learning. Nature Machine Intelligence. https://rdcu.be/ch6pL
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
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
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
Schnörr, (2020). Assignment Flows. Handbook of Variational Methods for Nonlinear Geometric Data. Springer. 235—260. https://www.springer.com/gp/book/9783030313500
Wolf, S, Hamprecht, F A and Funke, J (2020). Inpainting Networks Learn to Separate Cells in Microscopy Images. BMCVPDF icon Technical Report (357.23 KB)
Wolf, S, Hamprecht, F A and Funke, J (2020). Instance Separation Emerges from Inpainting. arXiv preprint arXiv:2003.00891
Wolf, S (2020). Machine Learning for Instance Segmentation. Heidelberg University
Wolf, S, Bailoni, A, Pape, C, Rahaman, N, Kreshuk, A, Köthe, U and Hamprecht, F A (2020). The Mutex Watershed and its Objective: Efficient, Parameter-Free Graph Partitioning. IEEE Transactions on Pattern Analysis and Machine Intelligence. 43 3724-3738PDF icon Technical Report (2.58 MB)
Bailoni, A, Pape, C, Wolf, S, Kreshuk, A and Hamprecht, F A (2020). Proposal-Free Volumetric Instance Segmentation from Latent Single-Instance Masks. GCPR. Springer. 12544 331-344
Wolf, S, Li, Y, Pape, C, Bailoni, A, Kreshuk, A and Hamprecht, F A (2020). The Semantic Mutex Watershed for Efficient Bottom-Up Semantic Instance Segmentation. ECCV. Proceedings. 208-224
Jähne, (2020). Struktur und Chaos: Kleinskalige Austauschprozesse zwischen Atmosphäre und Meer. Heidelberger Jahrbücher Online, Entwicklung – Wie aus Prozessen Strukturen werden. 5 133–150
2019
Schnörr, (2019). Assignment Flows. Variational Methods for Nonlinear Geometric Data and Applications. Springer
Kleesiek, J, Morshuis, J Nikolas, Isensee, F, Deike-Hofmann, K, Paech, D, Kickingereder, P, Köthe, U, Rother, C, Forsting, M, Wick, W, Bendszus, M, Schlemmer, H Peter and Radbruch, A (2019). Can Virtual Contrast Enhancement in Brain MRI Replace Gadolinium?: A Feasibility Study. Investigative Radiology. 54 653–660
Kiefer, L, Storath, M and Weinmann, A (2019). An efficient algorithm for the piecewise affine-linear Mumford-Shah model based on a Taylor jet splitting. IEEE Transactions on Image Processing. 29PDF icon Technical Report (2.04 MB)
Kirchhöfer, D M, Holst, G A, Wouters, F S, Hock, S and Jähne, B (2019). Extended noise equalisation for image compression in microscopical applications. tm - Technisches Messen. 86 422–432
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
Kirschbaum, E, Haußmann, M, Wolf, S, Sonntag, H, Schneider, J, Elzoheiry, S, Kann, O, Durstewitz, D and Hamprecht, F A (2019). LeMoNADe: Learned Motif and Neuronal Assembly Detection in calcium imaging videos. ICLR. Proceedings
Storath, M, Kiefer, L and Weinmann, A (2019). Smoothing for signals with discontinuities using higher order Mumford-Shah models. Numerische Mathematik. 143(2) 423-460PDF icon Technical Report (1.09 MB)
Esposito, M, Hennersperger, C, Göbl, R, Demaret, L, Storath, M, Navab, N, Baust, M and Weinmann, A (2019). Total variation regularization of pose signals with an application to 3D freehand ultrasound. IEEE Transactions on Medical Imaging. 38(10) 2245-2258
Ufer, N, Lui, K To, Schwarz, K, Warkentin, P and Ommer, B (2019). Weakly Supervised Learning of Dense SemanticCorrespondences and Segmentation. German Conference on Pattern Recognition (GCPR)PDF icon article (6.1 MB)
2018
Weilbach, C (2018). Dictionary Learning With Bayesian Gans For Few-Shot Classification. Heidelberg University
Wahl, A - S, Erlebach, E, Brattoli, B, Büchler, U, Kaiser, J, Ineichen, V B, Mosberger, A C, Schneeberger, S, Imobersteg, S, Wieckhorst, M, Stirn, M, Schroeter, A, Ommer, B and Schwab, M E (2018). Early reduced behavioral activity induced by large strokes affects the efficiency of enriched environment in rats. Sage Journals. Journal of Cerebral Blood Flow & Metabolism. http://journals.sagepub.com/doi/abs/10.1177/0271678X18777661PDF icon 0271678x18777661.pdf (770.87 KB)
Wahl, A - S, Erlebach, E, Brattoli, B, Büchler, U, Kaiser, J, Ineichen, V B, Mosberger, A C, Schneeberger, S, Imobersteg, S, Wieckhorst, M, Stirn, M, Schroeter, A, Ommer, B and Schwab, M E (2018). Early reduced behavioral activity induced by large strokes affects the efficiency of enriched environment in rats. Sage Journals. Journal of Cerebral Blood Flow & Metabolism. http://journals.sagepub.com/doi/abs/10.1177/0271678X18777661PDF icon 0271678x18777661.pdf (770.87 KB)
Haller, S, Swoboda, P and Savchynskyy, B (2018). Exact MAP-Inference by Confining Combinatorial Search With LP Relaxation. Thirty-Second AAAI Conference on Artificial Intelligence, (AAAI-18), New Orleans, Louisiana, USA, February 2-7, 2018. AAAI Press. https://www.aaai.org/ocs/index.php/AAAI/AAAI18/paper/view/16379PDF icon 2018-02-02_aaai_dense_combilp.pdf (325.08 KB)
Storath, M and Weinmann, A (2018). Fast median filtering for phase or orientation data. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40 639–652PDF icon Technical Report (7.32 MB)

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