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: TBA

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 2, 2021

Part one: Picturing Science: An Overview of Imaging Technologies

Part two: Novel Imaging Technologies: From Prototype to Product

Dr. Sima Salahshor

February 9, 2021

Part one: An Overview of the Fundamentals of Fluorescence Microscopy

Part two: Advanced imaging techniques: principles and applications

Dr. Sergio Grinstein, Paul Parouti and Dr. Kimberly Lau

The Hospital for Sick Children
University of Toronto, Department of Biochemistry

February 16, 2021

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

Dr. Ali Darbandi

The Hospital for Sick Children Research Institute

Advanced Bioimaging Centre
Departments of Biochemistry and Medical Biophysics

February 23, 2021

Microscopic Analysis and Interpretation in Veterinary Pathology

Dr. Susan Camilleri

The Centre for Phenogenomics Pathology Core, Mount Sinai Hospital

March 2, 2021

Application of Two-Photon Microscopy for Cellular Imaging and Photoactivation

Dr. Kenichi Okamoto and Dr. John Georgiou

Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute

March 9, 2021

How Artificial Intelligence (AI) Transforms Digital Pathology

Dr. Hamid Tizhoosh

Faculty of Engineering at the University of Waterloo

KIMIA Lab (Laboratory for Knowledge Inference in Medical Image Analysis)

Session details

February 2: Picturing Science and Novel Imaging Technologies

Led by Dr. Sima Salahshor

Part one: Picturing Science: An Overview of Imaging Technologies

Overview of the course and grant proposal writing, including:

  • the principles of market research
  • marketing
  • business development
  • IP rights
  • proposal writing
  • budget development
  • how to prepare compelling product pitches and to present proposals to funding agencies and private investors.

Part two: Novel Imaging Technologies: From Prototype to Product

A review of the latest imaging technologies used in clinics and research laboratories.

February 9: Fluorescence Microscopy and Advanced imaging techniques

Led by: Dr. Sergio Grinstein, Paul Parouti and Dr. Kimberly Lau

Part one: An Overview of the Fundamentals of Fluorescence Microscopy

The theoretical and practical aspects behind fluorescence microscopy, focusing on cellular imaging.

You will learn the basic principles and describe the equipment necessary to visualize fluorescently labelled specimens (both live and fixed). The topics featured will include:

  • the fundamentals of fluorophore absorption/excitation/emission
  • microscope and camera optics.

Part two: Advanced imaging techniques: principles and applications

We will focus on the principles behind two super-resolution microscopy technologies:

  1. Lightning (confocal microscopy with integrated deconvolution)
  2. Stimulated emission depletion (STED) microscopy.

These techniques enable image acquisition of both live and fixed specimens at resolutions of 1.5x – 4x greater than conventional fluorescence microscopy.

We will discuss the theory and application of these techniques then have a live demonstration.

February 16: Principle of Scanning (SEM) and Transmission Electron Microscopy (TEM)

Led by: Dr. Ali Darbandi

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

March 2: 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 infra-red light pulses, allowing photoactivation within a small volume.

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