JANEK GRÖHL
CURRICULUM VITAE
CURRICULUM VITAE
janekgroehl@live.de | |
@jgroehl | |
jgroehl |
Education
11/2016 - 04/2021 | Dr. sc. hum.: German Cancer Research Center (DKFZ) and Heidelberg University |
Thesis title: "Data-driven quantitative photoacoustic imaging" | |
Final grade: summa cum laude | |
09/2014 – 10/2016 | M.Sc. Medical Informatics: Heidelberg University, Heilbronn University, and the German Cancer Research Center (DKFZ) |
Thesis title: "Machine learning-based quantitative photoacoustic imaging" | |
Final grade: 1,1 | |
09/2011 – 08/2014 | B.Sc. Medical Informatics: Heidelberg University & Heilbronn University |
Thesis title: "Potential Analysis of Smart Glasses in Dermatology using the example of the Malignant Melanoma" | |
Final grade: 1,3 |
Research Experience
Since 02/2022 | Walter Benjamin Programme Fellow funded by the German Research Foundation (DFG) at Cancer Research UK, Cambridge Institute, University of Cambridge |
Since 07/2022 | By-Fellow at Hughes Hall College, University of Cambridge |
09/2021 - 09/2022 | Honorary Research Assistant at the Department of Medical Physics & Biomedical Engineering at University College London, UK |
12/2020 - 01/2022 | Research Associate at Bohndieklab, Cancer Research UK, Cambridge Institute |
02/2020-11/2020 | Postdoctoral Researcher at the German Cancer Research Center (DKFZ) Heidelberg |
Teaching Experience
Since 2022 | Lecturing on Medical Physics of Ultrasound Imaging for the Royal College of Radiologists |
Since 2021 | Supervision of research projects of students at the University of Cambridge (Part III Physics projects, MRes Mini Projects, Summer Internships) |
09/2020 - 08/2021 | Lectureship at Technische Hochschule Ulm (4 credit hours) |
2016 - 2020 | Supervision of Students at Heidelberg University (Internships, Bachelor theses, Master theses) |
06/2012 - 08/2013 | Seminar lecture for Mathematics (Analysis I & II) at Heilbronn University of Applied Sciences |
Fellowships, Grants, and Awards
02/2022 | Postdoctoral fellowship “Walter Benjamin Programme” of the German Research Foundation (DFG) |
07/2021 | NVIDIA Academic Hardware Grant (2x Quadro RTX 8000 and 1x Quadro RTX NVLink HB 2-Slot) |
03/2021 | Seal of Excellence by the European commission for project proposal 101023741, “PALPAITINE” submitted under the Horizon 2020’s Marie Skłodowska-Curie actions call H2020-MSCA-IF-2020 |
07/2018 | Best Poster Award: Annual PhD Retreat of the German Cancer Research Center |
04/2017 | 1st prize conhIT Nachwuchspreis 2017 for the master thesis “Machine learning based quantitative photoacoustic tomography” including a presentation at the conhIT 2017 conference |
04/2017 | Thomas-Gessmann-Special-Award for the master thesis “Machine learning based quantitative photoacoustic tomography” |
11/2016 | Three-year PhD Stipend of the Helmholz Graduate School for Cancer Research at the German Cancer Research Center |
10/2015 | Thomas-Gessmann-Award for the outstanding bachelor thesis „Potentialanalyse von SmartGlasses in der Dermatologie am Beispiel des malignen Melanoms“ |
09/2015 | One-year National Stipend of Heilbronn University and Dürr Dental AG |
09/2012 | Two-year National Stipend of Heilbronn University and the Thomas-Gessmann-Stiftung |
Conference Talks and Invited Talks
02/2024 | Two talks at SPIE Photonics West 2024 |
09/2023 | Invited Talk: “Data-driven quantitative photoacoustic imaging” Applied Inverse Problems |
02/2023 | Two talks and a poster at SPIE Photonics West 2023 |
10/2022 | Invited Talk: “Quantitative Photoacoustic Imaging” University of Zurich & ETH Zurich |
08/2022 | Invited Talk: “Quantitative Photoacoustic Tomography” Kings College London |
07/2022 | Invited Talk and plenary discussion char “Open Science and Sustainable Software for Data-driven Discovery” British Antarctic Survey |
06/2022 | Invited Talk: “Software Development with Open Science Principles” Edinburgh Napier University |
06/2022 | Invited Talk: “Towards data-driven quantitative photoacoustic imaging” Martin-Luther-University Halle-Wittenberg |
03/2021 | Conference Talk: “International photoacoustic standardisation consortium (IPASC): facilitation of international collaboration by means of a standardised metadata format for photoacoustic images” SPIE Photonics West |
04/2020 | Invited Talk: “Machine learning-based inference of functional tissue properties from multispectral photoacoustic imaging” at the OSA Biophotonics Congress |
04/2020 | Conference Talk: “International Photoacoustic Standardisation Consortium (IPASC): Progress in the data acquisition and management theme” SPIE Photonics West |
04/2020 | Conference Talk: “Deep learning-based oxygenation estimation for multispectral photoacoustic imaging” SPIE Photonics West |
11/2019 | Invited Talk: “Current Progress of the Data Acquisition and Management Theme” First IPASC Symposium |
04/2019 | Invited Talk: “Machine learning-based quantitative photoacoustic imaging” at the Biomedical Photonics Seminar at Bern University |
03/2019 | Conference Talk: “International Photoacoustic Standardisation Consortium (IPASC): recommendations for standardized data exchange in photoacoustic imaging” SPIE Photonics West |
12/2018 | Invited talk at a satellite event to the German Digital Summit organised by Siemens Healthineers |
02/2018 | Conference Talk: “Confidence estimation for quantitative photoacoustic imaging” SPIE Photonics West |
02/2018 | Conference Talk: “Reconstruction of initial pressure from limited view photoacoustic images using deep learning” SPIE Photonics West |
Commissions of Trust
02/2023 | Session Chair at the Photons Plus Ultrasound conference at SPIE Photonics West 2023 |
04/2022 | Associate Editor for the Journal Medical Physics |
Since 2021 | Administration of the bohndieklab.org website |
Since 2021 | Co-lead of an international project on the systematic comparison of image reconstruction algorithms for photoacoustic imaging |
Since 2018 | Regular reviewing of scientific articles for the following journals: Photoacoustics, IEEE Transactions on Medical Imaging, Journal of Biomedical Optics, Biomedical Optics Express, Applied Sciences, Sensors |
Since 2018 | Leadership team member of the International Photoacoustic Standardisation Consortium (IPASC) and Co-lead of the Data Acquisition and Management thematic working group |
Since 2018 | Design and administration of the ipasc.science website |
Peer Reviewed Articles
J Gröhl, TR Else, L Hacker, EV Bunce, PW Sweeney, SE Bohndiek. Moving beyond simulation: data-driven quantitative photoacoustic imaging using tissue-mimicking phantoms, IEEE Trans Med Imaging, 2023. |
J Gröhl*, L Hacker*, BT Cox, KK Dreher, S Morscher, A Rakotondrainibe, F Varray, LC Yip, WC Vogt, SE Bohndiek and International Photoacoustic Standardisation Consortium. The IPASC data format: A consensus data format for photoacoustic imaging. Photoacoustics, p.100339, 2022. *shared first authorship |
M Schellenberg, KK Dreher, N Holzwarth, F Isensee, A Reinke, N Schreck, A Seitel, MD Tizabi, L Maier-Hein* and J Gröhl*. Semantic segmentation of multispectral photoacoustic images using deep learning. Photoacoustics, p.100341, 2022. *shared senior authorship |
J Gröhl*, KK Dreher*, M Schellenberg, T Rix, N Holzwarth, P Vieten, L Ayala, SE Bohndiek, A Seitel, and L Maier-Hein. SIMPA: an open-source toolkit for simulation and image processing for photonics and acoustics. Journal of Biomedical Optics, 2022. *shared first authorship |
J Gröhl, T Kirchner, TJ Adler, L Hacker, N Holzwarth, A Hernández-Aguilera, MA Herrera, E Santos, SE Bohndiek, and L Maier-Hein. Learned spectral decoloring enables photoacoustic oximetry. Scientific reports, 11(1), pp.1-12, 2021. |
J Gröhl, M Schellenberg, KK Dreher, and L Maier-Hein. Deep learning for biomedical photoacoustic imaging: A review. Photoacoustics, p.100241, 2021. |
J Gröhl, T Kirchner, TJ Adler, and L Maier-Hein. Confidence estimation for machine learning-based quantitative photoacoustics. Journal of Imaging, 4(12):147, 2018. |
T Kirchner*, J Gröhl*, and L Maier-Hein. Context encoding enables machine learning-based quantitative photoacoustics. Journal of biomedical optics, 23(5):056008, 2018. *shared first authorship |
Peer Reviewed Co-Authorships
H Assi et al. A review of a strategic roadmapping exercise to advance clinical translation of photoacoustic imaging: From current barriers to future adoption. Photoacoustics, 2023. |
L Hacker et al. Fabrication of a Stable, Biologically Relevant Phantom Material. J of Visualized Experiments, 2023. |
M Schellenberg et al. Photoacoustic image synthesis with generative adversarial networks. Photoacoustics, 2022. |
EL Brown et al. Quantification of vascular networks in photoacoustic mesoscopy. Photoacoustics, 2022. |
L Maier-Hein et al. Heidelberg colorectal data set for surgical data science in the sensor operating room. Scientific data, 8(1), pp.1-11, 2021. |
T Kirchner et al. Photoacoustics can image spreading depolarization deep in gyrencephalic brain. Scientific reports, 9(1), pp.1-9, 2019. |
TJ Adler et al. Uncertainty-aware performance assessment of optical imaging modalities with invertible neural networks. International journal of computer assisted radiology and surgery, 14(6), pp.997-1007, 2019. |
T Kirchner et al. Se delay multiply and sum beamforming for multispectral photoacoustic imaging. Journal of Imaging, 4(10), p.121, 2018. |
M Klemm et al. MITK-OpenIGTLink for combining open-source toolkits in real-time computer-assisted interventions. International journal of computer assisted radiology and surgery, 12(3), pp.351-361, 2017. |
N Holzwarth et al. Tattoo tomography: Freehand 3D photoacoustic image reconstruction with an optical pattern. International Journal of Computer Assisted Radiology and Surgery, 16(7), pp.1101-1110, 2021. |
Preprints and Conference Proceedings
K Gu, K Yeung, M Doherty, L Hacker, TR Else, SE Bohndiek, J Gröhl. Long-short-term-memory cells enable flexible deep learning-based photoacoustic oximetry. Photons Plus Ultrasound: Imaging and Sensing, 2023. |
J Gröhl, L Hacker, BT Cox, International Photoacoustic Standardisation Consortium (IPASC): a structured comparison of photoacoustic image reconstruction algorithms. Photons Plus Ultrasound: Imaging and Sensing, 2022. |
J Gröhl, T Kirchner and L Maier-Hein. Confidence estimation for quantitative photoacoustic imaging. In Photons Plus Ultrasound: Imaging and Sensing 2018 (Vol. 10494, p. 104941C). International Society for Optics and Photonics, 2018. |
J Gröhl, T Kirchner, T Adler, L Maier-Hein. In silico 2D photoacoustic imaging data [Data Set]. zenodo archive. https://doi.org/10.5281/zenodo.1474258 |
Preprints and Conference Proceedings Co-Authorships
KK Dreher et al. Unsupervised domain transfer with conditional invertible neural networks. arXiv preprint arXiv:2303.10191, 2023 |
TR Else et al. The effects of skin tone on photoacoustic imaging and oximetry. bioRxiv, 2023.08. 17.553653, 2023 |
PW Sweeney et al. Segmentation of 3D blood vessel networks using unsupervised deep learning. bioRxiv, 2023.04. 30.538453, 2023. |
P Vieten et al. Deep learning-based semantic segmentation of clinically relevant tissue structures leveraging multispectral photoacoustic images. Photons Plus Ultrasound: Imaging and Sensing, 2022. |
JH Nölke et al. Invertible neural networks for uncertainty quantification in photoacoustic imaging. In Bildverarbeitung für die Medizin 2021 (pp. 330-335). Springer, Wiesbaden, 2021. |
SE Bohndiek et al. IPASC: A community-driven consensus-based initiative towards standardisation in photoacoustic imaging. In 2020 IEEE International Ultrasonics Symposium (IUS) (pp. 1-4). IEEE, 2020. |
TJ Adler et al. Uncertainty handling in intra-operative multispectral imaging with invertible neural networks. In International Conference on Medical Imaging with Deep Learning--Extended Abstract Track, 2019. |
LA Ayala et al. Live monitoring of Haemodynamic changes with Multispectral image analysis. In OR 2.0 context-aware operating theaters and machine learning in clinical Neuroimaging (pp. 38-46). Springer, Cham, 2019. |
T Kirchner et al. Photoacoustic monitoring of blood oxygenation during neurosurgical interventions. In Photons Plus Ultrasound: Imaging and Sensing 2019 (Vol. 10878, pp. 14-18). SPIE, 2019. |
T Kirchner et al. An open-source software platform for translational photoacoustic research and its application to motion-corrected blood oxygenation estimation. arXiv preprint arXiv:1901.09781, 2019. |
D Waibel et al. Reconstruction of initial pressure from limited view photoacoustic images using deep learning. In Photons Plus Ultrasound: Imaging and Sensing 2018 (Vol. 10494, p. 104942S). International Society for Optics and Photonics, 2018. |
L Maier-Hein et al. Crowd-algorithm collaboration for large-scale endoscopic image annotation with confidence. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 616-623). Springer, Cham, 2016. |