Fiosins

  • Tags: F
  • Mailadresse: Maksims Fiosins, PhD
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  • Datum + Kategorie: Post Doc

Khatri

  • Tags: K
  • Mailadresse: Robin Khatri, PhD
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  • Datum + Kategorie: Post Doc

Nosi

  • Tags: N
  • Mailadresse: Vladimir Nosi, PhD
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  • Datum + Kategorie: Post Doc

Testa

  • Tags: T
  • Mailadresse: Lucia Testa, PhD
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  • Datum + Kategorie: Post Doc

Zhao

  • Tags: Z
  • Mailadresse: Yu Zhao, PhD
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  • Datum + Kategorie: Post Doc

Zimmermann

  • Tags: Z
  • Mailadresse: Marina Zimmermann, PhD
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  • Datum + Kategorie: Assistant Professor

Marina Zimmermann

Group of Computational Pathology

Mission Statement

“Improve the understanding of diseases and their diagnosis through the automated analysis and quantification of microscopy images”

— Marina Zimmermann, PhD

Team Members

Research

The Group of Computational Pathology develops algorithms to analyse medical images, in particular microscopy images, in order to improve clinical diagnoses and advance the understanding of diseases. One of the focuses of our work is the quantitative analysis and discovery of signatures of diseases based on the segmentation of microscopy images with deep learning and classical image processing techniques. In order to achieve these goals, we collaborate closely with other groups at the HCKH and the UKE.

Marina Zimmermann, PhD

Assistant Professor 

Insitute of Medical Systembioinformatics, Center for Molecular Neurobiology(ZMNH),
III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE)
Martinistr. 52
20246 Hamburg, Germany

CV

  • Current Position

    since 2023 Assistant Professor for Computational Pathology, Institute of Medical Systems Biology (IMSB)

  • University Training

     2011 - 2013

    M.Sc. in Electrical and Electronics Engineering, Ecole polytechnique fédérale de Lausanne (EPFL), Switzerland
     2008 - 2011 B.Sc. in Electrical and Computer Engineering, Jacobs University Bremen, Germany

  • Academic qualifications

    2014 - 2018- 2020

    PhD in Electrical Engineering, Signal Processing Laboratory 5, Ecole polytechnique fédérale de Lausanne (EPFL), Switzerland, Supervisor: Prof. Jean-Philippe Thiran

  • Previous professional career

    Scientific postgraduate education:

    2021 - 2023 Team lead, Computational Pathology at Institute of Medical Systems Biology (IMSB), University Medical Center Hamburg-Eppendorf (UKE), Germany
    2018 - 2023

    Postdoctoral researcher, Institute of Medical Systems Biology (IMSB) and III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Germany
    2013 - 2018

    Research assistant, Signal Processing Laboratory 5, Ecole polytechnique fédérale de Lausanne (EPFL), Switzerland

  • Selected awards and honors

Selected publications

1.
Fuhlert P*, Westhaeusser F*, Dietrich E, Lennartz M, Khatri R, Kaiser N, Röbeck P, Bülow R, Von Stillfried S, Witte A, Ladjevardi S, Drotte A, Severgårdh P, Baumbach J, Puelles VG, Häggman M, Brehler M, Boor P, Walhagen P, Dragomir A, Busch C, Graefen M, Bengtsson E, Sauter G*, Zimmermann M*, Bonn S*. Med Image Anal. 2026 Feb;108:103884. 
2.
Lohmann JJG, Witte A, Maier A, Saak CC, Sauter G, Zimmermann M, Bonn S, Baumbach J. Array 2026, 29, 100725.
3.
Lahme K, Sachs W, Froembling S, Loreth D, Böttcher-Dierks V, Neumann K, Hann FM, Arkan N, Brehler M, Reichelt J, Sgries A, Surmann K, Gaffling S, Adler MR, Sáez PJ, Wedekind U, Lampert A, Tasika E, Saftig P, Conze C, Thünauer R, Skuza S, Neitzel K, Zielinski S, Brand J, Bonn S, Michalik S, Völker U, Zimmermann M, Wiech T, Meyer TN, Fester L, Meyer-Schwesinger C. Cell. 2026 Jan 8;189(1):123-142.e30. 
4.
Kuehl M, Okabayashi Y, Wong MN, Gernhold L, Gut G, Kaiser N, Schwerk M, Gräfe SK, Ma FY, Tanevski J, Schäfer PSL, Mezher S, Sarabia Del Castillo J, Goldbeck-Strieder T, Zolotareva O, Hartung M, Delgado Chaves FM, Klinkert L, Gnirck AC, Spehr M, Fleck D, Joodaki M, Parra V, Shaigan M, Diebold M, Prinz M, Kranz J, Kux JM, Braun F, Kretz O, Wu H, Grahammer F, Heins S, Zimmermann M, Haas F, Kylies D, Wanner N, Czogalla J, Dumoulin B, Zolotarev N, Lindenmeyer M, Karlson P, Nyengaard JR, Sebode M, Weidemann S, Wiech T, Groene HJ, Tomas NM, Meyer-Schwesinger C, Kuppe C, Kramann R, Karras A, Bruneval P, Tharaux PL, Pastene D, Yard B, Schaub JA, McCown PJ, Pyle L, Choi YJ, Yokoo T, Baumbach J, Sáez PJ, Costa I, Turner JE, Hodgin JB, Saez-Rodriguez J, Huber TB, Bjornstad P, Kretzler M, Lenoir O, Nikolic-Paterson DJ, Pelkmans L, Bonn S, Puelles VG.  Nature. 2025 Aug;644(8076):516-526. 
5.
Czogalla J, Hausmann F, Lagies S, Gies SE, Christiansen S, Kaiser N, Haas F, Okabayashi Y, Kylies D, Hofmann S, Franzin R, Sabra N, Bouari S, Fang Y, Ambagtsheer G, Edenhofer I, Chilla S, Mühlig AK, Zimmermann M, Wong MN, Yokoo T, Kretz O, Lindenmeyer M, Grahammer F, Hoogduijn MJ, de Bruin R, Kuehl M, Hänzelmann S, Kammerer B, Gesualdo L, Bonn S, Minnee RC, Huber TB, Puelles VG. JCI Insight. 2025 Sep 23;10(18):e190185. 
6.
Ragab H, Westhaeusser F, Ernst A, Yamamura J, Fuhlert P, Zimmermann M, Sauerbeck J, Shenas F, Özden C, Weidmann A, Adam G, Bonn S, Schramm C. Radiol Artif Intell. 2023 Apr 19;5(3):e220160.
7.
Kylies D, Zimmermann M, Haas F, Schwerk M, Kuehl M, Brehler M, Czogalla J, Hernandez L, Konczalla L, Okabayashi Y, Menzel J, Edenhofer I, Mezher S, Aypek H, Dumoulin B, Wu H , Hofmann S, Kretz O, Wanner N, Tomas N, Krasemann S, Glatzel M, Kuppe C, Kramann R, Benjamin B, Schneider R, Urbschat C, Arck P, Gagliani N, Wiech T, Grahammer F, Saez P, Wong MN, Bonn S, Huber TB, Puelles, VG.  Nat Nanotechnol. 2023 Apr;18(4):336-342.
8.

Deep learning-based molecular morphometrics for kidney biopsies.
Zimmermann M*, Klaus M*, Wong MN, Thebille AK, Gernhold L, Kuppe C, Halder M, Kranz J, Wanner N, Braun F, Wulf S, Wiech T, Panzer U, Krebs CF, Hoxha E, Kramann R, Huber TB*, Bonn S*, Puelles VG*. JCI Insight. 2021 Apr 8;6(7):e144779. 
9.
Thebille AK, Dietrich E, Klaus M, Gernhold L, Lennartz M, Kuppe C, Kramann R, Huber TB, Sauter G, Puelles VG, Zimmermann M*, Bonn S*. Annual Conference on Medical Image Understanding and Analysis 2021.
10.

Towards Explainable End-to-End Prostate Cancer Relapse Prediction from H&E Images Combining Self-Attention Multiple Instance Learning with a Recurrent Neural Network. Dietrich E, Fuhlert P, Ernst A, Sauter G, Lennartz M, Stiehl HS, Zimmermann M*, Bonn S*. Machine Learning for Health2021.

* Represents equal contributions as co-first or co-senior authors.

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Campus Research II N25
20246 Hamburg Germany
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