Microscopy Image Analysis

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Open Workshop on Microscopy Image Analysis in ITK and VTK

This workshop is part of the 2010_Summer_Project_Week at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK


If you would like to participate in this workshop then please:

  • Add your name to the "Participants" section below
  • Add your project to Microscopy Image Analysis projects list on the main page
  • Register for the overall conference from here
  • Create a wiki page describing your project following the preparation instructions on the 2010_Summer_Project_Week#Preparation home page and link this to your project listing


Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.


The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.


The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.


  • Monday afternoon- 1 slide lightning talk of project planned for the week using your project page
  • Wednesday afternoon - Microscopy Breakout Session ( Location: Kiva)
    • 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
      • 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
        • Sean Megason - Microscopy image analysis for into imaging of embryogenesis
        • Lydie Souhait - Demo of GoFigure
        • Arnaud Gelas - Interfacing with the Megason Lab
      • 1:20pm: Machiraju Lab- Ohio State Univ
        • Shantanu Singh - Large Scale Analysis of Cellular Phenotypes in the Tumor Microenvironment
        • Liya Ding - Image Analysis of Large Histology Datasets using ITK
      • 1:40pm: Palaniappan Lab- Univ of Missouri
      • 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
      • 2:20pm: Gouaillard Lab - Singapore Immunology Network
      • 2:40pm: Carolina Wahlby - Broad Institute
    • 2:45pm: Roundtable discussion of standards/interfaces
      • Image file types
      • Input-output interface for segmentation and tracking filters
      • Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
      • Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
      • Common human tasks
        • Manual segmentation and editing of results
        • Visualization of results
    • Future directions
  • Friday- 1 slide summary of results for the week using your project page
  • The rest of the time will be spent coding on projects


The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the Microscopy Image Analysis Project section of the main page


Please add your name to the list if you are interested in participating in this workshop

  1. Raghu Machiraju, Ohio State University
  2. Thierry Pecot, Ohio State University
  3. Shantanu Singh, Ohio State University
  4. Liya Ding, Ohio State University
  5. Kannappan Palaniappan, University of Missouri
  6. Ilker Ersoy, University of Missouri
  7. Adel Hafiane, ENSI-Bourges, France
  8. Yousef Al-Kofahi, Rensselaer Polytechnic Institute, CompuCyte Corporation
  9. Kedar Grama, Rensselaer Polytechnic Institute
  10. Raghav Padmanabhan, Rensselaer Polytechnic Institute
  11. Arnaud Gelas, Harvard Medical School
  12. Kishore Mosaliganti, Harvard Medical School
  13. Nicolas Rannou, Harvard Medical School
  14. Antonin Perrot-Audet, Harvard Medical School
  15. Lydie Souhait, Harvard Medical School
  16. Sean Megason, Harvard Medical School
  17. Luis Ibanez, Kitware
  18. Andinet Enquobahrie, Kitware
  19. Mathieu Malaterre, CoSMo
  20. Alex. Gouaillard. A*STAR / CoSMo
  21. Sonia Pujol. Brigham and Women's Hospital
  22. Steve Pieper, Isomics, Inc.
  23. Alex Yarmarkovich, Isomics, Inc.
  24. Curtis Lisle, KnowledgeVis
  25. Tammy Riklin Raviv, CSAIL, MIT
  26. Marc Niethammer, UNC Chapel Hill
  27. Carolina Wahlby, Broad Institute