PoL – Physics of Life | Publications


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

Labkit: Labeling and Segmentation Toolkit for Big Image Data
M Arzt, J Deschamps, C Schmied, T Pietzsch, D Schmidt, R Haase, F Jug
bioRxiv preprint https://doi.org/10.1101/2021.10.14.464362 (2021)

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

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

Open microscopy in the life sciences: Quo Vadis?
J Hohlbein, B Diederich, B Marsikova, EG Reynaud, S Holden, W Jahr, R Haase, K Prakash
arXiv preprint arXiv:2110.13951 (2021)

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

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

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

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

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

GPU-accelerating ImageJ Macro image processing workflows using CLIJ
D Vorkel, R Haase arXiv:2008.11799 arXiv (2020)

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

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

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

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

Star-convex polyhedra for 3d object detection and segmentation in microscopy
M Weigert, U Schmidt, R Haase, K Sugawara, G Myers
Proceedings of the IEEE/CVF Winter Conference on Applications of Computer … (2020)

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

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

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