Detailed Course Outline
Lectures and recommended papers for the Journal Clubs
(Please find the pdf versions of the papers listed as well as the tutorial at the “workshop resources” document, also posted)
November 6:
8:00-8:30 Welcome to CIHR Training Program
Questionnaire #1.
8:30-10:30 Lecture 1: Frank Somogy (General Manager, Microscopy Division,
Carl Zeiss Canada Ltd).
“Overview on Microscopy and Imaging”.
§ Introduction
o An introduction to the history and development of microscopy with particular emphasis on principals and techniques relevant to the biosciences
§ Principals of Wave Optics
o Duality of light (superposition),Newton and Huygens
o Image formation, light paths, magnification, scale, diffraction, wavelength
o Discussion of resolution( Raleigh’s Criterion), contrast, intensity information and phase information
§ Principals of Microscopy
o General
§ Lenses, aberrations and corrections
§ Standard Nomenclature
§ Parts of a microscope
§ Light sources and color temperature
o Transmitted Light Techniques
§ Brightfield (Koehler Illumination)
§ Phase Contrast (Cernike)
§ Darkfield
§ Polarization
§ Differential Interference Contrast (Nomarski)
o Reflected Light Techniques)
§ Fluorescence
§ Principals (Stokes)
§ Light Sources
§ Filters
§ Fluorochromes
10:30-12:30 Labs 1 and 2. (Frank Somogy and Darryl Dyck)
12:30-13:30 LUNCH
13:30-16:30 Labs 3, 4 and 5. (Frank Somogy and Darryl Dyck)
-Brief discussion of 1st workshop day.
November 7:
8:30-10:00 Lecture 2: Frank Somogy (General Manager, Microscopy Division,
Carl Zeiss Canada Ltd) and TBA.
“Live cell imaging”.
§ Live Cell Imaging
o Temperature control
§ Thermal stability, mass, and expansion
§ Stages and Environmental enclosures
§ Focus and movement
o PH control
§ Methods and requirements
§ Controllers
§ Custom chambers
§ Time Lapse
10:00-12:00 Lab 6: Live cell imaging. (Frank Somogy and Darryl Dyck)
12:00-13:00 LUNCH
13:00-14:30 Lecture 3: Dr. Peter Pennefather, University of Toronto
“Science with Conscience”.
14:30-16:30 Lecture 4: Dr. Catalena Birek, University of Manitoba
“Ethical Conduct for Research Involving Humans”.
-Brief discussion of 2nd workshop day.
16:30-18:30 Journal Club 1: Drs. Birek and Pennefather
Dr. Birek: TUTORIAL: Introduction to: The Canadian Tri-Council
Policy Statement: Ethical Conduct for Research
Involving Humans. (find the tutorial at the
“Workshop resources” document)
Dr. Pennefather: Paper for discussion:
1-Gorler J, Berghoff M, Kayser G and Kayser K (2006) Grid technology in tissue based diagnosis: fundamentals and potential developments Diagnostic Pathology 1:23 (24August) (pdf #1)
2-Petti C, Polage C, Quinn T, Ronald A, Sande M. Laboratory Medicine in Africa: A Barrier to Effective Health Care. Clinical Infectious Diseases, 2006:42, 377-382. (pdf #2)
November 8:
8:00-9:30 Lecture 5: Frank Somogy (General Manager, Microscopy Division,
Carl Zeiss Canada Ltd) and TBA.
“Digital Imaging and Documentation”.
§ Imaging and Documentation
o Photography
§ Film speed (DIN)
§ Film types
§ Focus and exposure
§ Issues with color film vs. B&W
§ Adaptors and vignetting
o Digital Imaging
· Information Management
§ Documentation and digital technology Chips, resolution, sensitivity and adaptors
§ Professional versus consumer cameras
§ Cooling and noise
§ Nomenclature and technology
§ File types and compression
9:30-11:00 Lab 7: Digital Imaging and Documentation. (Frank Somogy and
Darryl Dyck)
11:00-12:00 Lab 8: FISH experiment, day 1. (Dr. Mai’s lab)
12:00-13:00 LUNCH
13:00-16:30 Lab 8: FISH experiment, day 1, continuation. (Dr. Mai’s lab)
-Brief discussion of 3rd workshop day.
16:30-18:30 Journal Club 2: Dr. Sabine Mai.
Paper for discussion: -Weissleder R. Molecular Imaging in Cancer. Perspective. Science, 26 May, 2006, vol 312 (1168-1171) (pdf #3)
November 9:
8:30-10:00 Lecture 6: Veronica Karpiak, Cell Analysis and Imaging Field
Application Scientist. Invitrogen Corporation.
“Fluorescence probes for biological imaging”.
10:00-12:00 Lecture 7: Dr. Regen Drouin, University of Sherbrooke, Quebec.
“Fluorescence in situ hybridization (FISH): principles and the
different types of FISH as well as alternatives”.
12:00-13:00 LUNCH
13:00-14:00 Lab 9: FISH experiment, day 2, washes. (Dr. Mai’s lab)
14:00-15:30 Lecture 8: Dr. Ulrich Klingbeil, MetaSystems Group Inc.,
Boston, USA.
Automated sample analysis.
§ Screening Technologies
· Rare Cell Detection
· Metaphase Finding
· Spot counting
15:30-17:30 IMAGING at the Genomic Centre for Cancer
Research and Diagnosis (ON6026)
-Brief discussion of 4th workshop day.
17:30-19:00 Journal Club 3: Drs. Drouin and Klingbeil.
Dr. Drouin: Papers for discussion: -1. Speicher MR, Carter NP The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet. 2005; 6(10):782-92. Review. (pdf #4)
-2. Xu J, Chen Z Advances in molecular cytogenetics for the evaluation of mental retardation. Am J Med Genet C Semin Med Genet. 2003; 117(1):15-24. Review. (pdf #5)
Dr. Klingbeil: Papers for discussion: -Metafer a Novel Ultra High Throughput Scanning System for Rare Cell Detection and Automatic Interphase FISH Scoring.Macek M Sr, Bianchi D, Cuckle H (eds): Early Prenatal Diagnosis, Fetal Cells and DNA in the Mother, Present State and Perspectives. 12th Fetal Cell Workshop, Prague, May 2001. pp 329 – 339. (pdf #6)
November 10:
9:00-12:00 IMAGING at the Genomic Center for Cancer
Research and Diagnosis (ON6026).
12:00-13:00 LUNCH
13:00-16:00 IMAGING at the Genomic Center for Cancer
Research and Diagnosis (ON6026).
16:00-17:00 Selection of Images for Data discussion.
-Brief discussion of 5th workshop day.
November 11:
9:00-12:00 Data Discussion of selected Images
12:00-13:00 LUNCH
13:00-15:00 Questionnaire #2 and studying time
15:00-17:00 TEST