Essentials II – Essentials of confocal microscopy

Organizer: Manuel Gunkel, Aliaksandr Halavatyi, Marko Lampe and Christian Tischer

 Registration for EMBL staff only 

The course is a two day event and consists two practical sessions. The microscopy session covers the essential knowledge needed to conduct confocal microscopy-based experiments. Along with that, in a data handling and inspection session best practices of acquiring, handling and inspection of 3D image (volume) datasets with confocal microscopes are covered.
The microscope practical will be in the ALMF on January 19th (10 am to 5 pm).
Data handling and inspection together with CBA takes place on January 31st (2 to 5 pm).

The prerequisite for attending this course is the knowledge covered in Essentials I course. The microscopy knowledge covered in this is mandatory for introductions into ALMF Confocal-microscopes.

For preparation of the course you will get a short list of videos covering the basics as well as a self-test questionaire

Microscopy practical topics:

• Confocal principle
• Optical sectioning
• Confocal Lightpath
• Scanning
• Pinhole size
• Lateral and axial resolution
• 3D data acquisition with confocals
• Saturation and offset
• SNR Averaging/Accumulation, Voltage, laser power
• Refractive index and spherical aberrations
• Correcting for z-distortion
• Multicolor imaging
• Getting a transmitted light image with the confocal microscope
• Sample types

Data handling and ispection topics:

Using ImageJ, we will cover the following topics related to 3D image data:
• Orthogonal and arbitrary slice viewing
• 3-D rendering
• Reslicing
• Projections

Bookings