Plant imaging: advanced light microscopy - a joint course with CUSO MPS

8-9 March 2018

Organisers: Sonia Accossato (University of Neuchâtel), Dr. Sylvain Loubéry (University of Geneva) and Dr. Christoph Bauer (University of Geneva)



The course will focus on light microscopy, and the objective of the course is two-fold:

  • to acquire or strengthen basic knowledge of the most common methods of plant optical imaging (including sample preparation and staining)
  • to acquire or strengthen basic skills in image acquisition and in image analysis

The participants are expected to have prior experience with microscopy.



Part of the course will consist in lectures (basic and advanced optical microscopy, sample preparation, image analysis) and part of it will consist in hands-on sessions (confocal and widefield microscopy, image analysis).
During the hands-on sessions, all participants will use three different set-ups: a CLSM confocal, a spinning-disc confocal and a widefield microscope. Participants are welcome to bring their own samples.

This training course will be of value to anyone wanting to gain hands-on experience of modern confocal techniques. In addition to the hands-on component, the course will include tutorials on the theory and practice of current plant imaging techniques. The Plant Imaging Unit at UniGE is experimented in a variety of plant microscopy modalities. Participants will have the opportunity to exercise during the practical session.

Prerequisites: The participants are expected to have prior experience with microscopy. Participants will be asked to bring their own laptops for the image analysis hand-on session.



First day (8 March)

9h00: Registration

9h15-10h15: Introduction + participants talk (3 minutes/participant to describe his/her background and what are the techniques that are of particular interest to him/her)

10h15-10h30: Coffee break

10h30-12h00: Lecture "Fluorescence microscopy" (principles of widefield and confocal microscopes, acquisition parameters, deconvolution, light-sheet microscopy)

12h00-13h00: Lunch break

13h00-17h30: Hands-on in rotation in groups of 3: 1h30 on a classical confocal, 1h15 on a spinning-disc confocal, 1h15 on a widefield microscope (to see Koehler alignment, DIC setting, and how fluorescence filter cubes look like and how to change them)

Second day (9 March)

9h00-11h00: Lecture "Image analysis and Fiji"

11h00-11h15: Coffee break

11h15-12h15: External speaker or lecture "Sample preparation" (clearing methods, immuno-stainings, tips and tricks)

12h15-13h30: Lunch break

13h30-15h00: Hands-on "Image analysis and Fiji"

15h00-16h00: Debriefing/Final questions


Program (PDF)

General information

Date: 8-9 March 2018

Schedule: 9.00-17.30 (see program)

Venue: University of Geneva, Building “Sciences II/Sciences III”, quai Ernest-Ansermet 30, room tba

ECTS: 1.0 (Research tools)

Evaluation: Full attendance and active participation

Information: Please contact Sonia Accossato or the doctoral program coordinator Sara Santi (administration)

Registration fee: the course is free

Meals: The doctoral program in Organismal biology does not reimburse meal expenses

Travel expenses: For participants of the Interuniversity doctoral program in organismal biology (DP-biol ): see reimbursement conditions; for participants of the CUSO doctoral program in Molecular Plant Sciences: see CUSO MPS website

Make sure you sign the attendance list each and every day and take your attestation of attendance at the end of the course (no attestation will be sent by mail)


  • This course is free and open to all PhD students, however until 13 February 2018 priority is given to "Interuniversity doctoral program in organismal biology" and CUSO doctoral program in Molecular Plants Science participants who need microscopy skills for their current or future projects.
  • Post-docs are welcome as long as places are available.
  • Maximum number of participants: 9 people (minimum 6 people).
  • A waiting list will be prepared to ensure that there are no empty seats.

Registration through the web only: closed. The course is full.

Cancellation fee: before deadline: free of charge, after deadline: CHF 30.

Deadline: 20 February 2018