Confocal microscopy image formation
Prerequisites
Before starting this lesson, you should be familiar with:
Learning Objectives
After completing this lesson, learners should be able to:
Understand how the intensities in a digital image that was acquired with a confocal microscope are formed
Understand that the geometry of your biological specimen can have a large influence on these intensities
Motivation
In bioimage analysis one often wants to quantify the intensities in an image. To do this properly one needs to be aware that these intensities are influenced by many factors, making intensity quantification in general very difficult. Sometimes the measured intensities can be affected so much that even object shape measurements can become difficult. For all those reasons it is very important to understand the reasons for signal distortion! Not knowing those effects can easily lead to wrong measurements.
Concept map
Figure

Activities
- Open the zebrafish embryo image
- Inspect the image and appreciate that
- membranes appear with more contrast if they run along the optical axis
- signal decays within the specimen, due to scattering and absorption
- To do so, it is useful to slice the data along the x-z or y-z axis
Assessment
Fill in the blanks
- TODO ___ .
- TODO ___ .
Solution
- TODO
- TODO
Explanations
Follow-up material
Recommended follow-up modules:
Learn more: