PoL – Physics of Life | Publications

Publications

2022

J Hohlbein, B Diederich, B Marsikova, EG Reynaud, S Holden, W Jahr, R Haase, K Prakash. Open microscopy in the life sciences: Quo Vadis? Nat Methods 19, 1020–1025 (2022)
https://doi.org/10.1038/s41592-022-01602-3

FCMJM van Delft, A Månsson, H Kugler, T Korten, C Reuther, J Zhu, R Lyttleton, T Blaudeck, CR Meinecke, D Reuter, S Diez and H Linke. Roadmap for network-based biocomputation. Nano Futures 6 032002. (2022)
https://iopscience.iop.org/article/10.1088/2399-1984/ac7d81

R Haase, E Fazeli, D Legland, M Doube, S Culley, I Belevich, E Jokitalo, M Schorb, A Klemm, C Tischer. A Hitchhikers Guide through the Bio-image Analysis Software Universe. FEBS Letters (2022)
https://doi.org/10.1002/1873-3468.14451

A Schlaeppi, W Adams, R Haase, J Huisken, RB MacDonald, KW Eliceiri, EC Kugler. Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration. Front. Bioinform. (2022)
https://doi.org/10.3389/fbinf.2022.889755

M Arzt, J Deschamps, C Schmied, T Pietzsch, D Schmidt, R Haase, F Jug. Labkit: Labeling and Segmentation Toolkit for Big Image Data. Front. Comput. Sci. (2022)
https://doi.org/10.3389/fcomp.2022.777728

2021

R Haase. Image Processing Filters for Grids of Cells Analogous to Filters Processing Grids of Pixels. Front. Comput. Sci., (2021)
https://doi.org/10.3389/fcomp.2021.774396

J Girstmair, HK Moon, C Brillard, R Haase, P Tomancak. Time to Upgrade: A New OpenSPIM Guide to Build and Operate Advanced OpenSPIM Configurations. Advanced Biology (2021)
https://doi.org/10.1002/adbi.202101182

P Subramanian, S Gargani, A Palladini, M Chatzimike, M Grzybek, et al. The RNA binding protein HuR is a gatekeeper of liver homeostasis. Hepathology (2021)
https://doi.org/10.1002/hep.32153

R Haase. The Fiji Updater, My favorite image analysis tool, by Neubias members. Imaging and Microscopy.(2021)
https://analyticalscience.wiley.com/do/10.1002/was.0004000112

F Levet, AE Carpenter, KW Eliceiri, A Kreshuk, P Bankhead, R Haase. Developing open-source software for bioimage analysis: opportunities and challenges. F1000Research 10:302 (2021)
10.12688/f1000research.52531.1

GG Martins, FP Cordelières, J Colombelli, R D’antuono, O Golani, R Guiet et al. Highlights from the 2016–2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists. F1000Research 10:334 (2021)
10.12688/f1000research.25485.1

A Jain, V Ulman, A Mukherjee, M Prakash, MB Cuenca, LG Pimpale et al. Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation. Nat Commun 11, 5604 (2020)
10.1038/s41467-020-19356-x

D Kaptan, S Penkov, X Zhang, VR Gade, BK Raghuraman, R Galli et al. Exogenous ethanol induces a metabolic switch that prolongs the survival of Caenorhabditis elegans dauer larva and enhances its resistance to desiccation. Aging Cell, 19:e13214 (2020)
10.1111/acel.13214

D Vorkel, R Haase. GPU-accelerating ImageJ Macro image processing workflows using CLIJ. arXiv:2008.11799 arXiv preprint (2020) 
https://arxiv.org/abs/2008.11799

T Suckert, J Müller, E Beyreuther, B Azadegan, A Brüggemann, R Bütof et al. High-precision image-guided proton irradiation of mouse brain sub-volumes Radiotherapy and Oncology 146, 205–212 (2020)
10.1016/j.radonc.2020.02.023

R Bütof, S Löck, M Soliman, R Haase, R Perrin, C Richter, S Appold et al. Dose–volume predictors of early esophageal toxicity in non-small cell lung cancer patients treated with accelerated-hyperfractionated radiotherapy. Radiotherapy and Oncology 143, 44–50 (2020)
10.1016/j.radonc.2019.11.002

R Haase, A Jain, S Rigaud, D Vorkel, P Rajasekhar, T Suckert et al. Interactive design of GPU-accelerated Image Data Flow Graphs and cross-platform deployment using multi-lingual code generation bioRxiv preprint (2020) doi:
10.1101/2020.11.19.386565

R Haase, LA Royer, P Steinbach, D Schmidt, A Dibrov, U Schmidt et al. CLIJ: GPU-accelerated image processing for everyone. Nature methods 17 (1), 5–6 (2020)
10.1038/s41592-019-0650-1

M Weigert, U Schmidt, R Haase, K Sugawara, G Myers. Star-convex polyhedra for 3d object detection and segmentation in microscopy. Proceedings of the IEEE Workshop on Applications of Computer Vision (2020)
https://doi.org/10.48550/arXiv.1908.03636

2019

I Viktorinová, R Haase, T Pietzsch, I Henry, P Tomancak. Analysis of Actomyosin Dynamics at Local Cellular and Tissue Scales Using Time-lapse Movies of Cultured Drosophila Egg Chambers. Journal of visualized experiments: JoVE (2019)
10.3791/58587

A Bandurska-Luque, S Löck, R Haase, C Richter, K Zöphel, R Perrin et al. Correlation between FMISO-PET based hypoxia in the primary tumour and in lymph node metastases in locally advanced HNSCC patients. Clinical and translational radiation oncology 15, 108–112 (2019)
10.1016/j.ctro.2019.02.002

A Bandurska-Luque, S Löck, R Haase, C Richter, K Zöphel, N Abolmaali et al. FMISO-PET-based lymph node hypoxia adds to the prognostic value of tumor only hypoxia in HNSCC patients. Radiotherapy and Oncology 130, 97–103 (2019)
10.1016/j.radonc.2018.09.008