The Fundamentals of Optical Microscopy

NOTE: This course is an ONLINE EVENT

The Stem Cell Network, in collaboration with the Live Cell Imaging Laboratory at the University of Calgary, is pleased to offer the Fundamentals of Optical Microscopy course, targeted to trainees/HQP in the Stem Cell Network who are new to microscopy or want to brush up on their optical microscopy skills.

The course covers the essential concepts required to design and carry out fluorescence imaging experiments with a wide-field or confocal microscope. To maximize the transfer of learning to practice, participants will plan and present an imaging experiment directly related to their research.

This course is delivered in a blended format, combining live interactive Zoom sessions with three to four hours of independent work per week. The instructional team will provide support and guidance throughout. Participants who attend all live sessions and complete the independent work will be provided with a Certificate of Completion.

Learning objectives:

By the end of the online course, attendees should be able to:

  • Identify the key optical components in a standard fluorescence microscope and trace the light path
  • Interpret fluorescence spectra and match fluorescent probes with the appropriate filters for standard fluorescence experiments
  • Map out sample preparation for their own fluorescence microscopy experiments
  • Describe how to acquire fluorescence microscopy images using one or more fluorescent channels
  • Explain the difference between widefield and confocal microscopy and select the appropriate technique for a specific application
  • Apply best practices to optical microscopy experiments
  • Design an optical imaging experiment directly related to their research

Who Should Attend?
This microscopy course is designed for stem cell and regenerative medicine “wet bench” research trainees who are new to microscopy or want to brush up on their optical microscopy skills.

A research trainee is a graduate student, post-doc, research associate and/or technician currently working in the field of stem cells and regenerative medicine in a Canadian lab.

Course Format and Dates:

Module Topic Live session (delivery via Zoom) provisionally scheduled for 10:00-11:30 a.m. MT


Course welcome and community building Thursday, January 19


Introduction to fluorescence microscopy Thursday, January 26
3 Planning an imaging experiment and sample preparation Thursday, February 2
4 Designing a multi-colour imaging experiment Thursday, February 9
5 Introduction to magnification, resolution, and digital imaging Thursday, February 16
6 Successful image acquisition Thursday, February 23
7 Introduction to confocal microscopy Thursday, March 2
8 Best practices and case studies Last live session: Thursday, March 9
Course wrap-up Deadline for final report and reflection questions. All course work to be completed to achieve the Certificate of Completion Wednesday, March 22


Course Location: ONLINE. A link to the online sessions will be provided to successful applicants.

Application Procedure & Registration Fees

  1. Complete the application form here by 11:59 PM (sender’s time) Wednesday, November 30, 2022.
  2. Provide a full letter of support from your current supervisor detailing how your attendance will benefit your research and the lab’s stem cell research program as a whole. Letters should be e-mailed by supervisors directly to Ellie Arnold, earnold@stemcellnetwork.caat the same time you submit your application documents.
    A confirmation email will be sent within 24 hours of SCN receiving the submitted support letter. If a confirmation email is NOT received from SCN within 24 hours of submission, it is the responsibility of the applicant to contact SCN and ensure that all application materials have been received by SCN.
  3. The SCN Training & Education Committee will review all complete applications, and applicants will be informed of the competition outcome by December 14, 2022. Notification of acceptance for successful applicants will include a link for joining the online course sessions.

Spaces are limited for this important training opportunity. SCN will cover the registration costs (paid directly to the organizers) of this event for applicants from their networks who attend all sessions and complete all elements of the online content in this training event within the designated period. For applicants who fail to attend all sessions or complete the course content, in the absence of extenuating circumstances, a fee of $500 will be charged to their supervisor to cover the costs associated with delivering this training event.

Eligibility for the course:

  • Applicants must be a trainee / highly qualified personnel (HQP) (i.e. a graduate student, post-doc, research associate and/or technician) currently working on a research project in the field of stem cells and regenerative medicine in a Canadian lab. Non-academic applicants are welcome to apply, however academic applicants are prioritised. A $500 fee will apply to all non-academic applicants.
  • If you’re unsure whether you are a trainee / HQP, please email Ellie Arnold at for confirmation.
  • Applicants must clearly demonstrate that they will apply the techniques learned at the course to their own stem cell research project within one year.

Course Requirements:
Note that participants in this course are required to use their own laptop computers, with head-set for audio and webcam for video interaction. A second monitor/screen is also highly recommended.

Reporting and Communication Requirements:
By accepting a place on this course, the recipient agrees to complete a post-event survey describing the value of the training and networking opportunities made available through the course. This information will be used at SCN’s discretion on its website, newsletters and for the purpose of reporting to their funding agencies.

For further information on this course or for application related enquiries please contact Ellie Arnold at



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