LMP1100H: Cellular imaging in pathobiology

Who can attend

No specific courses are required; however, you should have successfully completed advanced courses in molecular biology, cell biology and/or biochemistry.

Priority will be given to more senior PhD students.

Course description

At the end of this course you will have:

  • acquired knowledge about different types of image analysis tools and software, microscopes, advanced imaging technologies and their functionality and use in biological sciences.
  • the knowledge and expertise to implement cutting edge microscopic and imaging methods within your laboratory.

This course explores the powerful intersection of Physics, Biological science, and Imaging technologies.

We focus on the theory, application and implementation of different imaging techniques, and more importantly, on the application of biological experimentation relevant to modern biological research or clinical, biochemical studies and the common real-life research goal in the industry, hospitals and research laboratories

We will cover the basic principles of optics such as:

  • Light
  • Diffraction
  • Refraction
  • The nature of lenses
  • The design of the light microscope
  • Latest image analysis tools
  • Artificial intelligence (AI), and machine learning software for image analysis
  • Digital pathology

We will discuss:

  • phase contrast
  • darkfield
  • interference contrast and modulation contrast
  • polarization
  • fluorescence microscopy

We will also cover different types of microscopes and imaging technologies and their use in biological sciences including:

  • Dissecting
  • Compound
  • Scanning and transmission electron microscopes
  • Positron emission tomography
  • Single-photon emission computed tomography
  • Nuclear magnetic resonance imaging
  • Ultrasound
  • Optical imaging
  • Stereology and 3d imaging
  • Optical microscopy
  • Nanoscopy
  • Live cell and whole animal imaging techniques
  • Cytogenetic
  • X-ray crystallography
  • Imaging in forensic science and their use in diagnostic pathology

You will be taught through lectures, online laboratory sessions demonstrating these systems and virtual research facility tours.

Course coordinators

Dr. Sima Salahshor


lmp.grad@utoronto.ca for administrative queries.

Timings and location

This course is offered in odd years (i.e. years ending in 1,3, etc.) in the Winter session.

Tuesdays 10 am - 12 pm

Location: MSB 2394

Evaluation methods

Participation in online lectures and live laboratory video sessions – 40%

Grant proposal – 40%

Writing a grant proposal

You will write a grant proposal consisting of the format:

  • Significance
  • Innovation
  • Approach
  • Financials
  • Product Summary

Your proposal should include at least one imaging technology.

Your proposal will be assessed based on scientific merit and judged based on:

  • how original the project is
  • how well the project is planned
  • how well the proposal budget is developed
  • what are the benefits that may result from this project?

You are encouraged to seek mentorship from an imaging technology expert for the specific method used in their grant proposal.


Also available in PDF format: lmp1100h-last_updated_dec2020.pdf




February 3, 2023

(1) Picturing Science: An Overview of Imaging Technologies.

(2) Novel Imaging Technologies: From Prototype to Product.

Dr. Sima Salahshor

February 14, 2023

Principle of Scanning (SEM) and Transmission Electron Microscopy (TEM).

Dr. Ali Darbandi

February 21, 2022

Digital Pathology and AI in Preclinical Studies, Translational Medicine and Clinical Practice.

Dr. Trevor McKee

February 28, 2023

Application of Two-Photon Microscopy for Cellular Imaging and Photoactivation

Dr. Kenichi Okamoto

Dr. John Georgiou

March 7, 2023

Introduction to Preclinical Imaging and STTARR Facility Tour- (Spatio-Temporal Targeting and Amplification of Radiation Response)

Dr. Warren Foltz, Deborah Scollard, Teesha Komal, Alex Wang, Dr. Luke Kwon, Dr. Naz Chaudary

March 14, 2023

Advances in Brain Imaging in Multiple Sclerosis; Preclinical, Diagnostic and Prognostic

Dr. Mohammad Ebrahimzdeh

Dr. Tae Joon (TJ) Yi

Session details