Skip to content. | Skip to navigation

Personal tools

Département de biologie
You are here: Home / Biology Master / Course List / Elective practical courses / Practicals in confocal microscopy and quantification in 2-4 dimensions

Practicals in confocal microscopy and quantification in 2-4 dimensions


Pradeep Das

3 crédits ECTS, 36h de TP


Objectives and organisation

This is an intensive training course on the cutting-edge techniques of optical microscopy.

The course will initially cover basic confocal but then swiftly move on to the more advanced techniques. Over the first few days, all participants will have seen several different confocal set-ups: a Leica SP8 with resonance scanning, as well as several Zeiss machines, such as the inverted LSM980 with Airyscan2, Elyra super-resolution and the upright LSM710. While the course is centred around optical microscopy, we will also carry out experiments using the JPK Nanowizard III atomic force microscope (AFM). Within each context, one or more types of experiments will be performed using different samples.

An essential feature of the course will lie in image analysis. We will use a number of analysis applications, including standard software such as ImageJ, as well as more specialized programmes (e.g. MorphoGraphX) and custom-made software pipelines (e.g. MARS and related python scripts) for performing full 3D reconstructions.

The course will be organised as a series of experimental ‘stations’, where students will work in groups of 2-3 to carry out various experiments based around a single coherent theme (e.g. mechanical biology). This will enable the groups to then share results obtained using diverse experimental approaches, in order to compare their technical outputs and to draw higher-level biological conclusions.

Several experts, notably from the PLATIM (the microscopy platform at the ENS) will guide and assist the course in various ways. Students who have been trained on specific microscopes (for example during one of their internships) will be allowed to assist their classmates on experiments at those stations.

In addition to the practical, laboratory-based work, the course will also feature classroom introductory sessions and student-led talks.






  • 60% continuous control, based on participation during the week, on ‘technical talks’ (on one of techniques seen during the week) and the final presentation (in groups) of the results obtained.
  • 40% final grade, based on a short, written report.