Anna Kreshuk

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Interdisciplinary Center for Scientific Computing (IWR)
Heidelberg Collaboratory for Image Processing (HCI)
Image Analysis and Learning Group
INF 205, 69120 Heidelberg

Tel.: +49 6221 5414804
e-mail: anna.kreshuk AT

Scientific Interests

I am interested in automating large-scale analysis of 3D Electron Microscopy volumes of neural tissue. Methodologically, this amounts to machine learning-based image processing. In particular, I am currently working on the introduction of higher-level priors into neuron segmentation algorithms. Previously, I did some research on synapse detection and segmentation and this topic is still of great interest to me. Do you find it exciting too? Come work with me, I'm looking for a PhD student!
More details can be found in the group's connectomics page and in the references listed below.


I am a visiting scientist at the HHMI Janelia Research Campus, where I collaborate with the groups of Davi Bock and Albert Cardona and the FlyEM Team Project.

Software projects

ilastik - interactive learning and segmentation toolkit. The github page is here.


  • since 2012 - PostDoc at HCI, University of Heidelberg
  • 2008-2011 - PhD Student at HCI, University of Heidelberg
  • 2007-2008 - Software developer, GSI Helmholtzzentrum fuer Schwerionenforschung, Darmstadt
  • 2004-2007 - Software developer for ROOT Project, CERN, Geneva, Switzerland
  • 1998-2003 - Diplom in Mathematics, Department of Mechanics and Mathematics, Lomonosov Moscow State University, Russia




  1. Kreshuk, A, Walecki, R, Köthe, U, Gierthmühlen, M, Plachta, D, Genoud, C, Haastert-Talini, K and Hamprecht, F A (2015). Automated Tracing of Myelinated Axons and Detection of the Nodes of Ranvier in Serial Images of Peripheral Nerves. Journal of Microscopy. 259 (2) 143-154
  2. Krasowski, N, Beier, T, Knott, G W, Köthe, U, Hamprecht, F A and Kreshuk, A (2015). Improving 3D EM Data Segmentation by Joint Optimization over Boundary Evidence and Biological Priors. 12th {IEEE} International Symposium on Biomedical Imaging, {ISBI} 2015, Brooklyn, NY, USA, April 16-19, 2015. 536-539
  3. Cali, C, Baghabra, J, Boges, D J, Holst, G R, Kreshuk, A, Hamprecht, F A, Srinivasan, M, Lehväslaiho, H and Magistretti, P J (2015). Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues. Journal of Comparative Neurology. 524 23-38
  4. Kreshuk, A, Funke, J, Cardona, A and Hamprecht, F A (2015). Who is talking to whom: synaptic partner detection in anisotropic volumes of insect brain. MICCAI. Proceedings. Springer. LNCS 9349 661-668
  5. Kreshuk, A, Köthe, U, Pax, E, Bock, D D and Hamprecht, F A (2014). Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks. PLoS ONE. 9 2
  6. Maco, B, Cantoni, M, Holtmaat, A, Kreshuk, A, Hamprecht, F A and Knott, G (2014). Semiautomated Correlative 3D Electron Microscopy of In Vivo Imaged Axons and Dendrites. Nature Protocols. 9 1354-1366
  7. Maco, B, Holtmaat, A, Cantoni, M, Kreshuk, A, Straehle, C N, Hamprecht, F A and Knott, G W (2013). Correlative in vivo 2 photon and focused ion beam scanning electron microscopy of cortical neurons. PloS one. 8 (2)
  8. Kreshuk, A, Straehle, C N, Sommer, C, Köthe, U, Cantoni, M, Knott, G and Hamprecht, F A (2011). Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images. PLoS ONE. 6 (10)
  9. Kreshuk, A, Stankiewicz, M, Lou, X, Kirchner, M, Hamprecht, F A and Mayer, M P (2010). Automated detection and analysis of bimodal isotope peak distribution in H/D exchange mass spectrometry using HeXicon. International Journal of Mass Spectrometry. 302 125-131