Anna Kreshuk

Anna Kreshuk
Education
Known forIlastik
Scientific career
Fields
Workplaces
ThesisAutomated Analysis of Biomedical Data from Low to High Resolution (2012)
Fred Hamprecht
WebsiteKreshuk Lab

Anna Kreshuk is a group leader at the European Molecular Biology Laboratory in Heidelberg, Germany. She joined the Cell Biology and Biophysics Unit in July 2018, where her group employs machine learning to develop automated methods to help biologists speed up image analysis.

Education

Kreshuk studied mathematics at the Lomonosov Moscow State University, finishing with a diploma in 2003. Before starting her Ph.D. studies, Kreshuk worked at CERN (2004–2007) and the GSI Helmholtz Centre for Heavy Ion Research (2007–2008) as a scientific programmer. From 2008 to 2011, she earned her Ph.D. in computer science, working at the Heidelberg Collaboratory for Image Processing (HCI) at the Heidelberg University, supervised by Prof Dr Fred Hamprecht.

Career and research

From 2012 to 2018, Kreshuk was employed at the Heidelberg Collaboratory for Image Processing (HCI) at the Heidelberg University, while pursuing her postgraduate studies.

Since 2018, Kreshuk has been a group leader at the European Molecular Biology Laboratory in Heidelberg, Germany.

Her research group has developed a toolkit for interactive learning and segmentation (Ilastik) to bring machine learning-based methods to members of the life science community without computer vision expertise.

Ilastik's algorithms are versatile and user-friendly, capable of addressing a broad range of image analysis issues. However, complex bioimage datasets often necessitate a more customized approach. Therefore, Kreshuk's team is especially focused on resolving intricate segmentation problems for 3D and large-scale light microscopy or electron microscopy (LM or EM). Recently, they've crafted techniques and tools for segmenting all cells and nuclei in a juvenile worm of the species Platynereis dumerilii (EM), as well as in various plant organs and tissues (LM).

Awards and honours

References

  1. 1 2 "Welcome: Anna Kreshuk". 20 April 2018.
  2. ↑ "Kreshuk Group – Machine learning for bioimage analysis".
  3. ↑ Kreshuk, Anna; Brun, R.; Antchevam, I.; Moneta, Lorenzo (2008). "ROOT Statistical Software". doi:10.5170/CERN-2008-001.179.
  4. ↑ Brun, R.; Canal, P.; Frank, M.; Kreshuk, A.; Linev, S.; Russo, P.; Rademakers, F. (2008). "Developments in ROOT I/O and trees". Journal of Physics: Conference Series. 119 (4) 042006. arXiv:0901.0886. Bibcode:2008JPhCS.119d2006B. doi:10.1088/1742-6596/119/4/042006.
  5. ↑ Antcheva, I.; Ballintijn, M.; Bellenot, B.; Biskup, M.; Brun, R.; Buncic, N.; Canal, Ph.; Casadei, D.; Couet, O.; Fine, V.; Franco, L.; Ganis, G.; Gheata, A.; Maline, D. Gonzalez; Goto, M.; Iwaszkiewicz, J.; Kreshuk, A.; Segura, D. Marcos; Maunder, R.; Moneta, L.; Naumann, A.; Offermann, E.; Onuchin, V.; Panacek, S.; Rademakers, F.; Russo, P.; Tadel, M. (2009). "ROOT — A C++ framework for petabyte data storage, statistical analysis and visualization". Computer Physics Communications. 180 (12): 2499–2512. arXiv:1508.07749. Bibcode:2009CoPhC.180.2499A. doi:10.1016/j.cpc.2009.08.005. S2CID 2616728.
  6. ↑ Kreshuk, Anna; Straehle, Christoph N.; Sommer, Christoph; Koethe, Ullrich; Cantoni, Marco; Knott, Graham; Hamprecht, Fred A. (2011). "Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images". PLOS ONE. 6 (10) e24899. Bibcode:2011PLoSO...624899K. doi:10.1371/journal.pone.0024899. PMC 3198725. PMID 22031814.
  7. ↑ Kreshuk, Anna; Koethe, Ullrich; Pax, Elizabeth; Bock, Davi D.; Hamprecht, Fred A. (2014). "Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks". PLOS ONE. 9 (2) e87351. Bibcode:2014PLoSO...987351K. doi:10.1371/journal.pone.0087351. PMC 3916342. PMID 24516550.
  8. ↑ Krasowski, N. E.; Beier, T.; Knott, G. W.; Kothe, U.; Hamprecht, F. A.; Kreshuk, A. (2018). "Neuron Segmentation with High-Level Biological Priors". IEEE Transactions on Medical Imaging. 37 (4): 829–839. Bibcode:2018ITMI...37..829K. doi:10.1109/TMI.2017.2712360. PMID 28600240. S2CID 4560617.
  9. ↑ The interactive learning and segmentation toolkit ilastik.org
  10. ↑ Berg, Stuart; Kutra, Dominik; Kroeger, Thorben; Straehle, Christoph N.; Kausler, Bernhard X.; Haubold, Carsten; Schiegg, Martin; Ales, Janez; Beier, Thorsten; Rudy, Markus; Eren, Kemal; Cervantes, Jaime I.; Xu, Buote; Beuttenmueller, Fynn; Wolny, Adrian; Zhang, Chong; Koethe, Ullrich; Hamprecht, Fred A.; Kreshuk, Anna (2019). "Ilastik: Interactive machine learning for (Bio)image analysis". Nature Methods. 16 (12): 1226–1232. doi:10.1038/s41592-019-0582-9. PMID 31570887. S2CID 203609613.
  11. ↑ Eisenstein, Michael (2023). "AI under the microscope: The algorithms powering the search for cells". Nature. 623 (7989): 1095–1097. Bibcode:2023Natur.623.1095E. doi:10.1038/d41586-023-03722-y. PMID 38012372.
  12. ↑ Vergara, Hernando M.; Pape, Constantin; Meechan, Kimberly I.; Zinchenko, Valentyna; Genoud, Christel; Wanner, Adrian A.; Mutemi, Kevin Nzumbi; Titze, Benjamin; Templin, Rachel M.; Bertucci, Paola Y.; Simakov, Oleg; Dürichen, Wiebke; Machado, Pedro; Savage, Emily L.; Schermelleh, Lothar; Schwab, Yannick; Friedrich, Rainer W.; Kreshuk, Anna; Tischer, Christian; Arendt, Detlev (2021). "Whole-body integration of gene expression and single-cell morphology". Cell. 184 (18): 4819–4837.e22. doi:10.1016/j.cell.2021.07.017. PMC 8445025. PMID 34380046.
  13. ↑ Wolny, Adrian; Cerrone, Lorenzo; Vijayan, Athul; Tofanelli, Rachele; Barro, Amaya Vilches; Louveaux, Marion; Wenzl, Christian; Strauss, Sören; Wilson-Sánchez, David; Lymbouridou, Rena; Steigleder, Susanne S.; Pape, Constantin; Bailoni, Alberto; Duran-Nebreda, Salva; Bassel, George W.; Lohmann, Jan U.; Tsiantis, Miltos; Hamprecht, Fred A.; Schneitz, Kay; Maizel, Alexis; Kreshuk, Anna (2020). "Accurate and versatile 3D segmentation of plant tissues at cellular resolution". eLife. 9 e57613. doi:10.7554/eLife.57613. PMC 7447435. PMID 32723478.
  14. ↑ "Hybrid Technologies for Structural Cell Biology at Near-Atomic Resolution".