Browse by Research Team

2024

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.
Müller, A. and Schmidt, D. and Albrecht, J.P. and Rieckert, L. and Otto, M. and Galicia Garcia, L.E. and Fabig, G. and Solimena, M. and Weigert, M.
Nature Protocols 29 February 2024 (In Press)

2023

ACTIS: improving data efficiency by leveraging semi-supervised augmentation consistency training for instance segmentation.
Rumberger, J.L. and Franzen, J. and Hirsch, P. and Albrecht, J.P. and Kainmueller, D.
In: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 02-06 Oct 2023, Paris, France. 25 December 2023

2022

RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. and Breimann, L. and Zouinkhi, M. and Epstein, L. and Kolyvanov, K. and Mamrak, N. and King, B. and Long, Xi and Harrington, K.I.S. and Lionnet, T. and Preibisch, S.
Nature Methods 19 (12): 1563-1567. December 2022

PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
Barbara, R. and Nagathihalli Kantharaju, M. and Haruvi, R. and Harrington, K. and Kawashima, T.
Frontiers in Cell and Developmental Biology 10 : 875044. 19 May 2022

PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
Barbara, R. and Nagathihalli Kantharaju, M. and Haruvi, R. and Harrington, K. and Kawashima, T.
bioRxiv : bioRxiv. 15 February 2022

LABKIT: labeling and segmentation toolkit for big image data.
Arzt, M. and Deschamps, J. and Schmied, C. and Pietzsch, T. and Schmidt, D. and Tomancak, P. and Haase, R. and Jug, F.
Frontiers in Computer Science 4 : 777728. 10 February 2022

The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L. and Morao, A.K. and Kim, J. and Jimenez, D.S. and Maryn, N. and Bikkasani, K. and Carrozza, M.J. and Albritton, S.E. and Kramer, M. and Street, L.A. and Cerimi, K. and Schumann, V.F. and Bahry, E. and Preibisch, S. and Woehler, A. and Ercan, S.
Journal of Cell Science 135 (2): jcs258818. January 2022

Mathematical and bioinformatic tools for cell tracking.
Hirsch, P. and Epstein, L. and Guignard, L.
In: Cell Movement in Health and Disease. Academic Press, London, 341-361. ISBN 978-0-323-90195-6 2022

2021

Patch individual filter layers in CNNs to harness the spatial homogeneity of neuroimaging data.
Eitel, F. and Albrecht, J.P. and Weygandt, M. and Paul, F. and Ritter, K.
Scientific Reports 11 (1): 24447. 27 December 2021

RS-FISH: Precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. and Breimann, L. and Zouinkhi, M. and Epstein, L. and Kolyvanov, K. and Long, X. and Harrington, K.I.S. and Lionnet, T. and Preibisch, S.
bioRxiv : 2021.03.09.434205v2. 18 October 2021

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L. and Dubois, Z. and Smith, J. and Lee, Y. and Harrington, K.
Biosystems 208 : 104483. October 2021

The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L. and Morao, A.K. and Kim, J. and Jimenez, D. and Maryn, N. and Bikkasani, K. and Carrozza, M.J. and Albritton, S.E. and Kramer, M. and Street, L.A. and Cerimi, K. and Schumann, V.F. and Bahry, E. and Preibisch, S. and Woehler, A. and Ercan, S.
bioRxiv : 2021.04.11.438056. 24 September 2021

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L. and Dubois, Z. and Smith, J. and Lee, Y. and Harrington, K.
bioRxiv : 2021.03.14.435300. 15 March 2021

3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells.
Müller, A. and Schmidt, D. and Xu, C.S. and Pang, S. and D'Costa, J.V. and Kretschmar, S. and Münster, C. and Kurth, T. and Jug, F. and Weigert, M. and Hess, H.F. and Solimena, M.
Journal of Cell Biology 220 (2): e202010039. 1 February 2021

DenoiSeg: joint denoising and segmentation.
Buchholz, T.O. and Prakash, M. and Schmidt, D. and Krull, A. and Jug, F.
Lecture Notes in Computer Science 12535 : 324-337. 10 January 2021

2020

Harnessing spatial homogeneity of neuroimaging data: patch individual filter layers for CNNs.
Eitel, F. and Albrecht, J.P. and Weygandt, M. and Paul, F. and Ritter, K.
arXiv : 2007.11899. 23 July 2020

CLIJ: GPU-accelerated image processing for everyone.
Haase, R. and Royer, L.A. and Steinbach, P. and Schmidt, D. and Dibrov, A. and Schmidt, U. and Weigert, M. and Maghelli, N. and Tomancak, P. and Jug, F. and Myers, E.W.
Nature Methods 17 (1): 5-6. January 2020

2019

A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage.
Sharir, A. and Marangoni, P. and Zilionis, R. and Wan, M. and Wald, T. and Hu, J.K. and Kawaguchi, K. and Castillo-Azofeifa, D. and Epstein, L. and Harrington, K. and Pagella, P. and Mitsiadis, T. and Siebel, C.W. and Klein, A.M. and Klein, O.D.
Nature Cell Biology 21 (9): 1102-1112. September 2019

2018

Content-aware image restoration: pushing the limits of fluorescence microscopy.
Weigert, M. and Schmidt, U. and Boothe, T. and Müller, A. and Dibrov, A. and Jain, A. and Wilhelm, B. and Schmidt, D. and Broaddus, C. and Culley, S. and Rocha-Martins, M. and Segovia-Miranda, F. and Norden, C. and Henriques, R. and Zerial, M. and Solimena, M. and Rink, J. and Tomancak, P. and Royer, L. and Jug, F. and Myers, E.W.
Nature Methods 15 (12): 1090-1097. December 2018

2014

Bridging the Gap: Methods and Teaching of F-A-S-T - Framing-Art-Science-Technology.
Schmidt, D. and Koalick, G. and Gassel, S. and Sery, C. and Groh, R. and Wacker, M.
Lecture Notes in Computer Science 8517 : 589-600. 2014

2013

Developing mobile interface metaphors and gestures.
Kammer, D. and Schmidt, D. and Keck, M. and Groh, R.
In: 15th International Conference on Human-Computer Interaction with Mobile Devices and Services, MobileHCI 2013, 27-30 August 2013, Munich, Germany. 27 August 2013