Cape Town 2025 workshop

Dates:
July 28 - August 1, 2025 Introduction to Principles of Microscopy
August 4 - 7th, 2025 Advanced Imaging Approaches for Fungal Pathogens 

Location: University of Cape Town, South Africa

Venue: Africa Microscopy Initiative

Event overview

This in-person joint training course is run by the Mycology Bioimaging Initiative, in partnership with the African Microscopy Initiative and the University of Cape Town’s IDM Microscopy Platform. The joint event will run July 28 - August 7, 2025, and comprises two courses: Introduction to Principles of Mycroscopy, followed by Advanced Imaging Approaches for Fungal Pathogens. 

Course aims: 

Introduction to Principles of Microscopy
This 5 day course offers foundational and hands-on training designed to enhance attendees microscopy knowledge, including technical knowledge and insights on basic and advanced microscopy techniques as well as quantitative data analysis.

Advanced Imaging Approaches for Fungal Pathogens

The 4-day Mycology Bioimaging course offers foundational and hands-on advanced training in fluorescence microscopy for studying pathogenic fungi and disease pathology. Participants will learn microscope fundamentals, fungal pathogen biology fundamentals, fluorescence reporter tools for visualizing subcellular compartments, and best practices for optimizing experimental conditions for fungal imaging. The course covers experimental setup, advanced imaging techniques like 3/4D cell culture, 3D tissue-level imaging, and single-cell analysis. Additionally, participants will be introduced to free advanced analysis tools such as FIJI, QuPath, and CellPose, as well as best practices for grant writing. This inaugural event aims to connect fungal cell biologists and medical mycologists, fostering a growing network of researchers using advanced bioimaging approaches in Africa to drive innovation in fungal pathogenesis research.

Note: This course will not provide training in drug susceptibility testing or routine diagnostic species identification. These skills can instead be acquired through these resources: ISHAM Diagnostics course , https://www.microfungi.net/ and here https://www.fun-mooc.fr/en/courses/medical-mycology/  

We will achieve this through the following activities:

• Free registration

• Optional (but strongly recommended) Fundamentals of Microscopy Workshop – Hosted by the African Microscopy Initiative and the University of Cape Town’s IDM Microscopy Platform.

• Meet the pathogen series – including key imaging applications and phenotypes

• Infection biology primers – Overview of key mammalian host cell players

• Tissue-level infection biology examples

• Hands-on mycology bioimaging experiment demos - at AMI microscopes

• Open source Image analysis & visualization showcase – Tools like Fiji, Cellpose, and QuPath

• Grant workshop session on microscopy & mycology-driven ideas 

• Opportunities for networking with other participants 

The tentative program will be available at a later stage.

This Mycology Bioimaging course is limited to 10 places and will take place in-person only.

Attendance fee

There are no registration costs associated with this event. Successful applicants will be encouraged to apply for a limited number of Travel Grants to cover specific expenses related to the event. 

Organizers

• Darren Thomson (MBI)

• Lucian Duvenage (MBI)

• Caron Jacobs (IDM)

• Elizabeth Ballou (MBI)

Prerequisites for application
You must currently reside in Africa and work, or plan to work, in Medical Mycology in Africa. You must have at least a Masters degree. We welcome fungal immunologists, pathologists, microbiologists, and cell biologists looking to expand into fungal pathogen research. This workshop is particularly suited for researchers wanting to leverage fluorescence microscopy technologies for grants, and especially those seeking to ask mechanistic questions about fungal pathogenicity. Clinicians interested in studying pathogenic traits of fungi with fluorescence microscopy are also encouraged to apply.

This is an advanced imaging courase and as such will not cover: 

• Routine diagnostic approaches

• MIC testing  

Application form

Please complete the application form at the following link to be considered for this course: APPLY HERE

Course application deadline: 9 March 2025

Travel grants

The Mycology BioImaging Initiative & Africa Microscopy Initiative are providing a limited number of travel grants for successful applicants who do not have institutional travel support to attend this course. 

Eligible travel grant costs include the following:

• Round-trip airline ticket

• Accommodation for the duration of the program

• Visa application fee 

Funds for air travel and visa fees will be disbursed in the form of reimbursements upon provision of reciepts. Accomodation will be provided for successful grant applicants. You will be responsible for ground transport to the accomodation and for any associated ground or air travel for visas related to the course. The event will be fully catered except for the evening of August 1st, or during the weekend of August 2-3, between the two courses.  

Travel grant application deadline: 31 March 2025

Please note that successful applicants to the course will be informed in time for the travel grant application deadline. 

 For any queries please contact Dr Darren Thomson at the MRC Centre for Medical Mycology at the University of Exeter: d.d.thomson@exeter.ac.uk

Upcoming events

What to expect from the workshop