Chair for Computer Aided Medical Procedures & Augmented Reality
Lehrstuhl für Informatikanwendungen in der Medizin & Augmented Reality

Hauptseminar/Master Seminar:
Microscopic Image Analysis

Nassir Navab, Diana Mateus, Laurent Demaret, Tingying Peng, Max Baust, Loic Peter

Type: Master Seminar Module IN2107
SWS: 2+0
ECTS: 4 Credits
Location: MI 03.13.010
Time: Tuesdays 10:00-12:00
Course Language: English


  • Introduction meeting will take place on the 22th of July at 10:00 in MI 03.13.010
  • The list of topics is available, ask the supervisors for login and password to access the material
  • First preliminary meeting will take place on the 9th of July at 11:30 in MI 03.13.010
  • Registration through TUMOnline.

Contents and Objectives

Microscopy is a main source of knowledge for the discovery of complex interactions between biological agents, which are used in modern medical research for  the development of new diagnostics and therapeutics. In recent years automated image processing techniques  have gained in importance  for the understanding of microscopic data, permitting to overcome the time bottleneck due to the the size of the data and the complexity of the interactions. In this seminar, students will be exposed to recent advances in microscopy image acquisition, processing and analysis. Students will learn about:

  • different microscopy imaging modalities, such as bright-field, confocal, dark-field, digital, electron, fluorescence, phase contrast and X-ray.
  • image analysis methods for detection, classification, segmentation and registration of diverse observed entities, e.g. tissues, cells, molecules, proteins, among others.


The seminar consists of a preliminary meeting, an introductory meeting and seminar sessions. Each of the sessions will consist of ~3 student presentations. All seminar participants are expected to be present at every session and to actively participate in the discussion.

Each student is asked to select one topic from a list. In order to successfully complete the seminar, participants have to fullfill these requirements:

  • Presentation: The selected paper is presented to the other participants (20 minutes presentation 10 minutes questions). Use the CAMP templates for PowerPoint CAMPmaster.pot, or Latex: CAMP-latex-template.zip.
  • Written Handout: A document of maximum 8 pages is written and submitted one week after the presentation. Please download and use the llncs2e.zip Latex template. The handout must include all references used and must be written completely in your own words. Copy and paste will not be tolerated. The handout has to be written in English.
  • Attendance: Participants have to participate actively in all seminar sessions. Each presentation is followed by a discussion and everyone is encouraged to actively participate.


The seminar consists of a preliminary meeting, an introductory meeting and seminar sessions. Each of the sessions will consist of several student presentations. All seminar participants are expected to be present at every session and to actively participate in the discussion.


Info Meeting Slides

List of Topics

Please find below the list of topics for this semester. Send your choice by email to Diana Mateus. First-come, first-served!

Date Student Tutor Topic Papers
Nov 19 Jun Shen DM Cell detection and segmentation I
 tmi 2012 Attributed Relational Graphs for Cell Nucleus Segmentation in Fluorescence Microscopy Images
Nov 19 Radu Diaconescu DM Cell Detection and segmentation II
 miccai 2013 Automated Nucleus and Cytoplasm Segmentation of Overlapping Cervical Cells
 cvpr 2013 Learning to Detect Partially Overlapping Instances
Nov 19 Bibiana do Canto Angense MB Cell Detection and segmentation III
 iccv 2009 Fast Ray Features for Learning Irregular Shapes
 isbi 2010 Cell Segmentation in Microscopy Imagery using a Bag of Local Bayesian Classifiers
Dec 3 Adrià Puigdomènech Badia LP 2D+time segmentation
 Algorithms 2012 Parallel Algorithms for Segmentation of Cellular structures in 2D+time and 3D morphogenesis data
Dec 3 Mohamed Ragab MB Cell Tracking I
 MedIA 2008 Cell Population Tracking and Lineage Construction with Spatiotemporal Context
Dec 3 David Ngyuen LP Mitosis Detection
 tmi 2011 Automated Mitosis Detection of Stem Cell Populations in Phase-Contrast Microscopy Images
Dec 17 Katharina Kann LP Histology classification and quantification I
 tmi 2007 Multifeature Prostate Cancer Diagnosis and Gleason Grading of Histological Images
  Shanmugapriya Survarachakan (canceled) LD Histology classification and quantification II
 tmi 2009 Automatic Classification for Pathological Prostate Images Based on Fractal Analysis
Dec 17 Christian Rupprecht TP Histology classification and quantification IV
 cvpr 2012 Multiple Clustered Instance Learning for Histopathology Cancer Image Classification, Segmentation and Clustering
 miccai 2012 Structure and Context in Prostatic Gland Segmentation and Classification
Jan 14 Mark Muth TP 3D histology reconstruction
 JPathInfo 2013 3D Reconstruction of Multiple Stained Histology Images
Jan 14 Dinh Nguyen LD Denoising
 micron 2012 A median-Gaussian filtering framework for Moiré pattern noise removal from X-ray microscopy image
Jan 14 Patmaa Sridharan LD Restoration
 miccai 2012 Phase Contrast Image Restoration Via Dictionary Representation of Diffraction Patterns
 miccai 2013 Efficient Phase Contrast Microscopy Restoration Applied for Muscle Myotube Detection
- - - Cell Tracking II  cvpr 2008 General Constraints for Batch Multiple-Target Tracking Applied to Large-Scale Videomicroscopy
 nips 2011 Structured Learning for Cell Tracking
- - - Histology classification and quantification III  tmi 2011 Weighted Maximum Posterior Marginals for Random Fields Using an Ensemble of Conditional Densities From Multiple Markov Chain Monte Carlo Simulations

Literature and Helpful Links

A lot of scientific publications can be found online.

The following list may help you to find some further information on your particular topic:

Some publishers:

Libraries (online and offline):

Some further hints for working with references:

  • JabRef is a Java program for comfortable working with Bibtex literature databases. Handy feature: if you know the PubMed ID for an article, JabRef can import data from there (via "Web Search/Medline").
  • Mendeley is a cross-platform program for organising your references.

If you find useful resources that are not already listed here, please tell us, so we can add them for others. Thanks.

Title: Microscopy Image Analysis
Professor: Nassir Navab
Tutors: Diana Mateus, Laurent Demaret, Tingying Pen, Loic Peter
Type: Hauptseminar
Term: 2013WiSe

Edit | Attach | Refresh | Diffs | More | Revision r1.31 - 13 Dec 2013 - 09:23 - DianaMateus

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