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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.
A. Andersson, Diego, F., Hamprecht, F. A., and Wählby, C., “ISTDECO: In Situ Transcriptomics Decoding by Deconvolution”, bioRxiv, 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.
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.
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.
F. C. Walter, Damrich, S., and Hamprecht, F. A., “MultiStar: Instance Segmentation of Overlapping Objects with Star-Convex Polygons”, ISBI. pp. 295-298, 2021.PDF icon Technical Report (1.83 MB)
D. Kotovenko, Wright, M., Heimbrecht, A., and Ommer, B., “Rethinking Style Transfer: From Pixels to Parameterized Brushstrokes”, Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR). 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.
B. Brattoli, Büchler, U., Dorkenwald, M., Reiser, P., Filli, L., Helmchen, F., Wahl, A. - S., and Ommer, B., “Unsupervised behaviour analysis and magnification (uBAM) using deep learning”, Nature Machine Intelligence, 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.
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.
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.
C. Schnörr, “Assignment Flows”, Handbook of Variational Methods for Nonlinear Geometric Data. Springer, p. 235—260, 2020.
S. Wolf, Hamprecht, F. A., and Funke, J., “Inpainting Networks Learn to Separate Cells in Microscopy Images”, BMCV. 2020.PDF icon Technical Report (357.23 KB)
S. Wolf, Hamprecht, F. A., and Funke, J., “Instance Separation Emerges from Inpainting”, arXiv preprint arXiv:2003.00891, 2020.
S. Wolf, “Machine Learning for Instance Segmentation”. Heidelberg University, 2020.
S. Wolf, Bailoni, A., Pape, C., Rahaman, N., Kreshuk, A., Köthe, U., and Hamprecht, F. A., “The Mutex Watershed and its Objective: Efficient, Parameter-Free Graph Partitioning”, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 43, pp. 3724-3738, 2020.PDF icon Technical Report (2.58 MB)
A. Bailoni, Pape, C., Wolf, S., Kreshuk, A., and Hamprecht, F. A., “Proposal-Free Volumetric Instance Segmentation from Latent Single-Instance Masks”, GCPR, vol. 12544. Springer, pp. 331-344, 2020.
S. Wolf, Li, Y., Pape, C., Bailoni, A., Kreshuk, A., and Hamprecht, F. A., “The Semantic Mutex Watershed for Efficient Bottom-Up Semantic Instance Segmentation”, ECCV. Proceedings. pp. 208-224, 2020.
B. Jähne, “Struktur und Chaos: Kleinskalige Austauschprozesse zwischen Atmosphäre und Meer”, Heidelberger Jahrbücher Online, Entwicklung – Wie aus Prozessen Strukturen werden, vol. 5. pp. 133–150, 2020.
2019
C. Schnörr, “Assignment Flows”, Variational Methods for Nonlinear Geometric Data and Applications. Springer, 2019.
J. Kleesiek, 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., “Can Virtual Contrast Enhancement in Brain MRI Replace Gadolinium?: A Feasibility Study”, Investigative Radiology, vol. 54, pp. 653–660, 2019.
L. Kiefer, Storath, M., and Weinmann, A., “An efficient algorithm for the piecewise affine-linear Mumford-Shah model based on a Taylor jet splitting”, IEEE Transactions on Image Processing, vol. 29, 2019.PDF icon Technical Report (2.04 MB)
D. M. Kirchhöfer, Holst, G. A., Wouters, F. S., Hock, S., and Jähne, B., “Extended noise equalisation for image compression in microscopical applications”, tm - Technisches Messen, vol. 86, pp. 422–432, 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.
E. Kirschbaum, Haußmann, M., Wolf, S., Sonntag, H., Schneider, J., Elzoheiry, S., Kann, O., Durstewitz, D., and Hamprecht, F. A., “LeMoNADe: Learned Motif and Neuronal Assembly Detection in calcium imaging videos”, ICLR. Proceedings. 2019.
M. Storath, Kiefer, L., and Weinmann, A., “Smoothing for signals with discontinuities using higher order Mumford-Shah models”, Numerische Mathematik, vol. 143(2), pp. 423-460, 2019.PDF icon Technical Report (1.09 MB)
M. Esposito, Hennersperger, C., Göbl, R., Demaret, L., Storath, M., Navab, N., Baust, M., and Weinmann, A., “Total variation regularization of pose signals with an application to 3D freehand ultrasound”, IEEE Transactions on Medical Imaging, vol. 38(10), pp. 2245-2258, 2019.
N. Ufer, Lui, K. To, Schwarz, K., Warkentin, P., and Ommer, B., “Weakly Supervised Learning of Dense SemanticCorrespondences and Segmentation”, in German Conference on Pattern Recognition (GCPR), 2019.PDF icon article (6.1 MB)
2018
C. Weilbach, “Dictionary Learning with Bayesian GANs for Few-Shot Classification”, Heidelberg University, 2018.
A. - S. Wahl, 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., “Early reduced behavioral activity induced by large strokes affects the efficiency of enriched environment in rats”, Sage Journals, vol. Journal of Cerebral Blood Flow & Metabolism, 2018.PDF icon 0271678x18777661.pdf (770.87 KB)
A. - S. Wahl, 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., “Early reduced behavioral activity induced by large strokes affects the efficiency of enriched environment in rats”, Sage Journals, vol. Journal of Cerebral Blood Flow & Metabolism, 2018.PDF icon 0271678x18777661.pdf (770.87 KB)
S. Haller, Swoboda, P., and Savchynskyy, B., “Exact MAP-Inference by Confining Combinatorial Search With LP Relaxation”, in Thirty-Second AAAI Conference on Artificial Intelligence, (AAAI-18), New Orleans, Louisiana, USA, February 2-7, 2018, 2018.PDF icon 2018-02-02_aaai_dense_combilp.pdf (325.08 KB)
M. Storath and Weinmann, A., “Fast median filtering for phase or orientation data”, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 3, pp. 639–652, 2018.PDF icon Technical Report (7.32 MB)

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