Postdocs (current)

PhD students (current)

• Denis Barucic

Researchers

Postdocs (former)

• Thomas Dietenbeck
  Reseach project: "Microscopy image analysis"
  Thomas obtained his PhD from CREATIS, INSA Lyon, France. He worked on neuronal fiber tracking.
  Publications.

• Miroslav Hekrdla
  Miroslav comes from the radar industry. He worked on the analysis of the carotid images.
  Publications.

• Jan Hering
  Reseach project: "Detection of myeloma from low-dose CT images"
  Jan has obtained his PhD from the University of Heidelberg. He was working on multiple myeloma detection by multiple instance learning.
  Publications.

• Sumit Kaushik
  Sumit has obtained his PhD from the Masaryk University in Brno.
  Publications.

• Francisco Martínez
  Reseach project: "Detection of myeloma from low-dose CT images"
  Publications.

• Rodrigo Uriel Nava
  Reseach project: "Automatic analysis of spatial gene expression patterns for Drosophila"
  Publications.

• François Varray
  Reseach project: "Microscopy image analysis"
  Thomas obtained his PhD from CREATIS, INSA Lyon, France. He worked on neuronal fiber tracking.
  Publications.

• Jan Švihlík
  Reseach project: "Analysis of microscopy images of Langerhans islets"
  Jan works on analyzing microscopic images of Langerhans islets.
  Publications.

PhD students (former)

• Martin Dolejší
  Reseach project: "Registration of histology slices"
  Martin worked on nodule detection from CT.
  Publications.

• Muhamad Khodadadi Azadboni
  Reseach project: "Microscopy image analysis"
  Muhamad will mainly work on classification from microscopy images.

• Guorong Yu
  Reseach project: "Geometric graph matching"
  Guorong was a long-term visiting PhD student from Wuhan University.
  Publications.

• Jiří Borovec (graduated 2018)
  Reseach project: "Registration of histology slices"
  Publications.

• Miguel Amável Pinheiro (graduated 2017)
  Reseach project: "Geometric graph matching"
  Miguel is supported by a Portuguese government grant. He focuses on the problem of registering tree-like structures.
  Publications.

• Juan David García-Arteaga (graduated 2013)
  Reseach projects: "Elastic image registration", "Automatic malaria diagnosis from microscopy images"
  Juan David is now a post-doc in Colombia.
  Publications.

• Marián Uherčík (graduated 2011)
  Reseach project: "Tool detection in 3D ultrasound"
  Co-supervised with Christian Cachard and Hervé Liebgott.
  Publications.

• Jef Vandemeulebroucke (graduated 2010)
  Reseach project: "Respiratory motion estimation"
  Currently at Brussels University. Co-supervised with Patrick Clarysse and David Sarrut.
  Publications.

• Martin Barva (graduated 2007)
  Currently working for Deutsche Börse Group in Frankfurt am Main, Germany
  Publications.

• Jan Petr (graduated 2007)
  Reseach project: "Parallel MRI reconstruction"
  Currently a post-doc in Helmholtz center, Dresden. Formerly a post-doc with the VISAGE team at INRIA, Rennes, France.
  Publications.

• Jakub Krátký
  Reseach project: "3D medical image segmentation"
  Jakub is now working for one of the Prague hospitals.
  Publications.

Researchers (former)

• Martin Dolejší
  Reseach projects: "Detection of lung nodules from CT", "Registration of histology slices"
  Martin was working as a scientific programmer.
  Publications.

Master students (MSc/Ing/Mgr)

• Martin Kostelanský "Localization and segmentation of in-vivo ultrasound carotid artery images" (graduated 2021)
  Publications.

• Jan Kúdelka "Classification of tumor type from histopathological images" (graduated 2021)
  Publications.

• Hana Mertanová "Cell segmentation in microscopy using a reference modality" (graduated 2021)
  Publications.

• Jakub Maly "Automatic event recognition for Higgs boson detection" (graduated 2020)
  Publications.

• Petr Kočiš "Vessel detection and red blood cells velocity estimation algorithm for microcirculation analysis" (graduated 2019)

• Hanna Hlushak "Accuracy evaluation of Langerhans islet volume estimation from microscopic" (graduated 2016)
  Publications.

• Iva Latnerova "Reduction of False Positives in Lung Nodule Detection Algorithm" (graduated 2014)
  Reseach project: "Detection of lung nodules from CT"
  Iva has worked on improving the quality of lung nodules detection.

• Martin Hrubý "Detection of changes in 3D MRI data using image registration" (graduated 2009)
  Reseach project: "Elastic image registration"
  Publications.

• Marián Pauco "Cryogel phantoms for ultrasound elastography" (graduated 2009)
  Reseach project: "Ultrasound elastography"
  Publications.

• Ivo Čermák "The class of oil purity II" (graduated 2009)
  Reseach project: "Detection of impurities in oil in microscopy images"
  Supervised by Martin Novotný, I was a consultant.
  Publications.

• Vít Špringl "Automatic Malaria Diagnosis through Microscopy Imaging" (graduated 2009)
  Reseach project: "Automatic malaria diagnosis from microscopy images"
  Publications.

• Helena Jansová "Reconstruction of 3D surface from colonoscopic video" (graduated 2008)
  Reseach project: "Colonoscopy image analysis"
  Publications.

• Tomáš Kazmar "Opacity Quantification in Cardiac Angiogram Sequence" (graduated 2008)
  Reseach project: "Opacity quantification in cardiac angiogram sequence"
  from the Faculty of Mathematics and Physics, Charles University (MFF UK).
  Publications.

• Jiří Mazanec "Viewer and Segmentation Tool for 3D MRI data" (graduated 2008)
  Reseach project: "3D medical image segmentation"
  Publications.

• Martin Dolejší "Lung nodule detection" (graduated 2007)
  Reseach project: "Detection of lung nodules from CT"
  Martin is continuing towards a PhD (see above)

• Marek Jasanský "Parallelization of The EEG Forward Problem by The Boundary Element Method" (graduated 2007)
  Reseach project: "MEG/EEG reconstruction"
  Publications.

• Jiří Svoboda "Entropy estimation methods comparison for image registration" (graduated 2007)
  Reseach project: "High dimensional mutual information estimation"
  Publications.

• Sudershan Sundararajan "Colour Image Registration" (graduated 2005)
  Reseach project: "High dimensional mutual information estimation"
  Publications.

Bachelor students (BSc/Bc)

• Radka Olyšarová "Automatic estimation of hdEEG electrode positions" (2021)
  Publications.

• Branislav Doubek "Implementation of Multiple Instance Learning using Markov Networks." (2020)
  Publications.

• Pavlína Koutecká "Automatic Detection of Metastases in Whole-Slide Lymph Node Images Using Deep Neural Networks" (2020)
  Publications.

• David Kunz "Robust and Fast Local All Pass Image Registration" (2020)
  David Kunz worked on implementing the sparse local all pass registration algorithm.
  Publications.

• Vojtěch Poříz "Diabetic Retinopathy Detection Using Neural Networks" (2020)
  Publications.

• Maria Dobko "Lung nodule and cancer detection in computed tomography scans using deep learning." (2019)
  Publications.

• Bohdan Petryshak "Segmentation using CNN and shape priors" (2019)
  Publications.

• Jiří Kaňka "Automatic evaluation of gel electrophoresis images" (2008)
  Reseach project: "Analysis of images from gel electrophoresis"

• Barbora Vrbová "Analysis of images from gel electrophoresis" (2008)
  Reseach project: "Analysis of images from gel electrophoresis"

Short-term project students

(Mostly one semester projects.)

• Ana Manzano (2021)
  Ana is a visiting student from UPC, working on predicting changes in carotid artery ultrasoud images.
  Publications.

• Vatsal Goel (2019)
  Summer internship student, worked on recurrent visual attention models for histopathology images.
  Publications.

• Jeremy Bonnin (2017)
  Jeremy is a visiting master student from ENSTA Brest, France, working on microscopy image classification.

• Carlos Sanchez (2017)
  Carlos is a visiting PhD student from Madrid, working on combining multiple microscopy images.

• Atin Mathur "Segmentation and registration." (2013)
  Reseach project: "Registration of histology slices"
  Internship.

• Jatin Mehta "Segmentation of bone-cartilage-soft tissue interfaces from ultrasound." (2013)
  Reseach project: "Analysis of ultrasound images of the knee"
  Internship.

• Ardhendu Shekhar Tripathi "Segmentation and registration." (2013)
  Reseach project: "Registration of histology slices"
  Internship.

• Sova Jan "Acquisition of ultrasound RF signals." (2009)

• Mirza Pasovič "Ultrasound propagation. Segmentation using message passing." (2009)
  PhD visitor.

• Martinez Francisco "Image Segmentation in 3D with Graph Cuts." (2007)
  ERASMUS exchange.

• Hora Ivo "DICOM medical image viewer." (2007)

• Gažák Petr "Automated visual classication of malaria infected cells." (2007)
  Co-supervised with Juan David García.

• Špringl Vít "Automated malaria diagnosis through microscopy imaging." (2007)
  Co-supervised with Juan David García.

• Ignacio Arganda-Carreras "Bidirectional elastic registration." (2006)
  PhD visitor.
  Publications.

• Martin Hrubý "MRI data preprocessing for registration." (2006)

• Mazanec Jiří "3D viewer for MRI data." (2006)

• Jasanský Martin "Proposal for parallelization of the BEM method." (2006)
  Reseach project: "MEG/EEG reconstruction"

• Jan Hrdlička "3D visualization and shape analysis of nerve fibres" (2005)

• Jiří Svoboda "Detection of nerves and blood vessels from ultrasound sequences" (2005)

Collaborators (former)

• Michal Bušta was a programmer working on a microscopy image registration project.
• Jana Podlipská was a PhD student from Oulu, Finland, that I was collaborating with.
• Archibald Pontier was a PhD student supervised by my colleague Boris Flach.