BS6218 - Advanced Cell Imaging and Image Analysis

Summary of co​urse content

This course is the specialization electives for the Biotechnology track.

In this advance cell imaging learning course, you will learn different types of light- and electron microscopes (EM). You will have several hands-on sessions to collect image data from the different light microscopes, including confocal laser microscopy, total internal reflection fluorescence microscopy, wide-field microscopy, light-sheets microscope, etc.

You will receive a detailed introduction of the top-notch focused ion beam (FIB)-coupled cryo-electron microscope (CryoEM) setup, EM sample preparation, and tomograph data analysis. You will learn the quantitative imaging analysis skill and understand how the machine-learning could be engaged for biological imaging data. You will be taught and directly supervised by the faculty, experts in advanced imaging technologies for fundamental biology and biomedical research.

Rationale for introducing this course

Biological imaging is a major research field in data science. Fluorescence-based light microscopy and EM imaging technology create a large volume of data requiring machine learning-based analysis, one of the major interdisciplinary biomedical research. Understanding the data acquisition in imaging biological samples is critical knowledge to understand the integration of data science 2D- or 3D-imaging data set. It requires structured, systematic understanding and logical thinking to be used towards problem-solving.

This course will guide the student to solve the problem in real-world scenarios, which is the gap between computing skill and analysis of biological images. This course aims to address these issues by exposing students to various biological data and conventional data analysis approaches for advanced cell images or movies. If successful, the students may be placed on a clear career trajectory early in their graduate training.

Aims and objectives

  • You will learn to use and choose different advanced light microscopes in a competitive real-world setting
  • You will learn about the quantitative analysis of the biological image and movie, 2D- or 3D-imaging dataset
  • Via experiential learning in teams (2-3), you will acquire the necessary hard and soft skills (e.g. dada analysis, teamwork, communication, leadership and grit) necessary for successful outcomes

    • Syllabus

    Fundamental and application of fluorescent microscope with data analysis

    1. Fundamental of microscopic imaging (Fluorescence Signals, Spectra, Detection, Resolution, Magnification etc) (TEL)
    2. Introduction to Fluorescence Microscopic imaging (STED, SIM, PALM, STORM, TIRF, Confocal laser scanning microscopy (CLSM) and Spinning-disk confocal microscopes, Correlative light and electron microscopy) (TEL)
    3. Quantitative fluorescence Image Analysis (3D reconstruction, pattern analysis, single particle analysis, FRAP, FRET etc)
    4. Introduction of Deep learning-based image analysis
    5. The Confocal Fluorescence Microscope
    6. Super-resolution microscope and application (Aryscan etc)
    7. Light Sheets Microscope and application (LSM and LLSM)

    8. Practical sessions for different light microscopy (involve industrial partnership, ZEISS or Microlambda Pte Ltd.

    Electron Microscopy

    9. Basic principles of TEM (TEL)
    10. Single Particle EM vs 3D electron tomography
    11. Conventional (room-temperature) TEM vs cryo-EM
    12. Cry Focused Ion Beam Milling and Cryo electron tomography
    13. Analysis of cryo electron tomography data
    14. Introduction of sample preparation and imaging for advanced cryo-EM (On-site demonstration in imaging facilities)

     

    Assessment

    CA (Presentation of computational modelling, AI-based data analysis, and application)
    		Individual40%
    Participation (Imaging sample preparation; in-class discussion)
    		Individual20%
    Assignment (Data analysis and report)Group20%
    Assignment (Data acquisition in practical session)Group20%
    Total 100%

     

    ​​​Hours of Contact/ Academic Units: 39 hours / 3 AU

    Instructor and Co-instructor (if any):

    • Assoc Prof Miao Yansong (Course Coordinator)
    • Assoc Prof Li Hoi Yeung;
    • Asst Prof Alexander Ludwig;

    • Assoc Prof Lu Lei

    Class size: 10-40