Browse by Research Team

Article

miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner.
Cerda Jara, C.A., Kim, S.J., Thomas, G., Farsi, Z., Zolotarov, G., Dube, G., Deter, A., Bahry, E., Georgii, E., Woehler, A., Piwecka, M. and Rajewsky, N.
EMBO Reports 25 (7): 3039. July 2024

RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E., Breimann, L., Zouinkhi, M., Epstein, L., Kolyvanov, K., Mamrak, N., King, B., Long, Xi, Harrington, K.I.S., 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., Nagathihalli Kantharaju, M., Haruvi, R., Harrington, K. and Kawashima, T.
Frontiers in Cell and Developmental Biology 10 : 875044. 19 May 2022

LABKIT: labeling and segmentation toolkit for big image data.
Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D., Tomancak, P., 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., Morao, A.K., Kim, J., Jimenez, D.S., Maryn, N., Bikkasani, K., Carrozza, M.J., Albritton, S.E., Kramer, M., Street, L.A., Cerimi, K., Schumann, V.F., Bahry, E., Preibisch, S., Woehler, A. and Ercan, S.
Journal of Cell Science 135 (2): jcs258818. January 2022

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

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

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

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

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

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

Book Section

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

Conference or Workshop Item

ACTIS: improving data efficiency by leveraging semi-supervised augmentation consistency training for instance segmentation.
Rumberger, J.L., Franzen, J., Hirsch, P., 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

Developing mobile interface metaphors and gestures.
Kammer, D., Schmidt, D., 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

Review

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.
Müller, A., Schmidt, D., Albrecht, J.P., Rieckert, L., Otto, M., Galicia Garcia, L.E., Fabig, G., Solimena, M. and Weigert, M.
Nature Protocols 19 (5): 1436-1466. May 2024

Letter

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

Preprint

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