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 senior PhD students.

Course description

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

We will cover 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, modulation contrast, polarization and fluorescence microscopy.
  • 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, live cell and whole animal imaging techniques and their use in diagnostic pathology.

This course will 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.

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: See schedule below.

Evaluation methods

60% Participation in lectures and laboratory sessions

40% Grant proposal


You can download the schedule in a PDF format.

Date and location



February 7, 2023

Room 2394

Medical Sciences Building (MSB)

Picturing Science: An Overview of Imaging Technologies.

Breaking Down Tissue: HALO Quantitative Tissue Analysis.

Dr. Sima Salahshor

Dr. Amber L. Ortiz, Spencer Revill and Maciej Zerkowski

February 14, 2023

Room 06-9701 and 06-9621

686 Bay Street

The Hospital for Sick Children Research Institute

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

Dr. Ali Darbandi

February 21, 2022

Room 2394

Medical Sciences Building (MSB)

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

Dr. Trevor McKee

February 28, 2023

Room 3214

Medical Sciences Building (MSB)

Application of Two-Photon Microscopy for Cellular Imaging and Photoactivation

Dr. Kenichi Okamoto

Dr. John Georgiou

March 7, 2023

Room 7-211

101 College Street, East Elevators, 7th Floor, STTARR, MaRS

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

Room 2394

Medical Sciences Building (MSB)

Magnetic Resonance Imaging: Diagnostic and Prognostic Biomarkers of Multiple Sclerosis

Dr. Mohammad Ebrahimzdeh

Dr. Tae Joon (TJ) Yi

Session details

February 7: Picturing Science: An Overview of Imaging Technologies

Led by Dr. Sima Salahshor

We will review some of the latest imaging technologies used in clinics and research laboratories.

February 14: Principle of Scanning (SEM) and Transmission Electron Microscopy (TEM)

Led by: Dr. Ali Darbandi

We will discuss general principles underlying electron microscopes and differences between scanning and transmission microscopes.

February 28: Application of Two-Photon Microscopy for Cellular Imaging and Photoactivation

Led by: Dr. Kenichi Okamoto and Dr. John Georgiou

Two-photon microscopy is suitable for deep tissue imaging using infrared light pulses, allowing photoactivation within a small volume.

This lecture will outline two-photon microscopy principles and demonstrate applications of live photoactivation techniques combined with imaging of fluorescent probes in living brain sections.

We will also discuss molecular and cellular imaging, two-photon photoactivation of protein activity and imaging at the synapse level.

March 7: Introduction to Preclinical Imaging and STTARR Facility Tour- (Spatio-Temporal Targeting and Amplification of Radiation Response)

Led by: Dr. Warren Foltz, Deborah Scollard, Teesha Komal, Alex Wang, Dr. Luke Kwon, and Dr. Naz Chaudary

This lecture will explore the application of in-vivo imaging techniques (MRI, CT, PET/SPECT, IGRT, ultrasound, and optical imaging) in preclinical research.

Scaled down, high resolution versions of these imaging systems are used at STTARR to visualize small-animal models of disease and evaluate the efficacy of corresponding diagnostic and therapeutic methods.

March 14: Magnetic Resonance Imaging - Diagnostic and Prognostic Biomarkers of Multiple Sclerosis

Led by: Dr. Mohammad Ebrahimzdeh and Dr. Tae Joon (TJ) Yi

This lecture will cover two areas:

  1. an overview of the histopathological and clinical manifestations of multiple sclerosis (MS)
  2. the utility of magnetic resonance imaging (MRI) in research and clinical practice in the MS therapeutic area.

MS is a debilitating chronic autoimmune disease of the central nervous system (CNS; brain, spinal cord, and optic nerve, etc) that can lead to impairment of vision, memory, balance, and mobility. These impairments are hypothesized to be, at least in part, the result of myelin sheath damage, following immune cell infiltrations of the CNS.

The myelin sheath is the protective outer layer of nerve fibers. Since the myelin is necessary for the transmission of nerve impulses through nerve fibers, their damage will disrupt the transmission of nerve impulses. The areas of myelin damage in the CNS are called inflammatory demyelinating lesions.

Recent advancements in MRI technology have made it possible to visualize these lesions and other biomarkers of MS. As such MRI is quickly emerging as an important paraclinical tool for diagnosis, prognosis, monitoring disease progression, and treatment-response assessments.

The use of MRI in research studies has advanced our understanding of disease mechanisms underlying the histopathology of MS.