Anna Kreshuk Explained

Anna Kreshuk
Thesis Title:Automated Analysis of Biomedical Data from Low to High Resolution
Thesis Url:https://archiv.ub.uni-heidelberg.de/volltextserver/14498/
Thesis Year:2012
Doctoral Advisor:Fred Hamprecht
Known For:Ilastik
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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.[1] [2]

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)[3] [4] [5] 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.[6]

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.[7] [8] Since 2018, Kreshuk has been a group leader at the European Molecular Biology Laboratory in Heidelberg, Germany.[1]

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.[9] [10] [11]

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),[12] as well as in various plant organs and tissues (LM).[13]

Kreshuk is a well-known computer scientist. Hence, she is frequently invited to workshops,[14] seminars,[15]

Awards and honours

Notes and References

  1. Web site: Welcome: Anna Kreshuk . 20 April 2018 .
  2. Web site: Kreshuk Group – Machine learning for bioimage analysis .
  3. Web site: ROOT Statistical Software . 10.5170/CERN-2008-001.179 . 2008 . Kreshuk . Anna . Brun . R. . Antchevam . I. . Moneta . Lorenzo .
  4. Developments in ROOT I/O and trees . 10.1088/1742-6596/119/4/042006 . 2008 . Brun . R. . Canal . P. . Frank . M. . Kreshuk . A. . Linev . S. . Russo . P. . Rademakers . F. . Journal of Physics: Conference Series . 119 . 4 . 042006 . 0901.0886 . 2008JPhCS.119d2006B .
  5. ROOT — A C++ framework for petabyte data storage, statistical analysis and visualization . 10.1016/j.cpc.2009.08.005 . 2009 . 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. . Computer Physics Communications . 180 . 12 . 2499–2512 . 1508.07749 . 2009CoPhC.180.2499A . 2616728 .
  6. 10.1371/journal.pone.0024899 . free . Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images . 2011 . Kreshuk . Anna . Straehle . Christoph N. . Sommer . Christoph . Koethe . Ullrich . Cantoni . Marco . Knott . Graham . Hamprecht . Fred A. . PLOS ONE . 6 . 10 . e24899 . 22031814 . 2011PLoSO...624899K . 3198725 .
  7. 10.1371/journal.pone.0087351 . free . Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks . 2014 . Kreshuk . Anna . Koethe . Ullrich . Pax . Elizabeth . Bock . Davi D. . Hamprecht . Fred A. . PLOS ONE . 9 . 2 . e87351 . 24516550 . 2014PLoSO...987351K . 3916342 .
  8. Neuron Segmentation with High-Level Biological Priors . 2018 . 10.1109/TMI.2017.2712360 . 28600240 . Krasowski . N. E. . Beier . T. . Knott . G. W. . Kothe . U. . Hamprecht . F. A. . Kreshuk . A. . IEEE Transactions on Medical Imaging . 37 . 4 . 829–839 . 4560617 .
  9. https://www.ilastik.org/ The interactive learning and segmentation toolkit
  10. Ilastik: Interactive machine learning for (Bio)image analysis . 10.1038/s41592-019-0582-9 . 2019 . 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 . Nature Methods . 16 . 12 . 1226–1232 . 31570887 . 203609613 .
  11. 10.1038/d41586-023-03722-y . AI under the microscope: The algorithms powering the search for cells . 2023 . Eisenstein . Michael . Nature . 623 . 7989 . 1095–1097 . 38012372 . 2023Natur.623.1095E . free .
  12. 10.1016/j.cell.2021.07.017 . Whole-body integration of gene expression and single-cell morphology . 2021 . 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 . Cell . 184 . 18 . 4819–4837.e22 . 34380046 . 8445025 .
  13. 10.7554/eLife.57613 . free . Accurate and versatile 3D segmentation of plant tissues at cellular resolution . 2020 . 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 . eLife . 9 . 32723478 . 7447435 .
  14. Web site: Deep learning for image analysis – Course and Conference Office .
  15. Web site: Biophysics & Development Seminar: Anna Kreshuk, EMBL .
  16. Web site: Hybrid Technologies for Structural Cell Biology at Near-Atomic Resolution .

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