Biomicroscopy I

Lectures:

Starting on September 9th

Where: Auditorium DIA 005

• Nikita Glebov: nikita.glebov@epfl.ch
• Berkay Dagli: berkay.dagli@epfl.ch
• Xinyi Huang: xinyi.huang@epfl.ch

Course summary: Understand the principles of optical microscopes, their limitations, and their advantages by using geometrical and wave optics. Introduce commonly used biomicroscopy methods such as wide-field and fluorescence. Cover basic microscopy components for investigating biological samples.

Course content: Ray (geometrical) optics; Matrix (ABCD) optics; Wave optics;  Fourier optics; Magnification in microscopy and optical design; Resolution in microscopy, e.g. point-spread function (PSF); Contrast in microscopy; Wide-field microscopy; Fluorescence microscopy principles and examples;  Microscopy elements: objectives, eyepiece, filters, sources, detectors.

Learning Outcomes: 

• Sketch basic optical systems
• Characterize the elements of a microscope
• Estimate the resolution of imaging systems
• Understand wide-field microscopy, fluorescence microscopy
• Propose a suitable microscopy configuration for imaging a sample.

Evaluation: Written exam (multiple-choice test) during the final exam session

Consultation session:
Room: 
Date and time: 

Exam Information:

Room: 

Date and time: 

Exam rules:

• Provide ALL your final answers on the answer sheets, and indicate your name on each page.
• Pages without a name or unreadable will be discarded and will NOT count for the exam.
• Write in a readable manner and answer the questions precisely.
• Allowed support: Notes are allowed only to bring TWO A4 papers. You can use the back-side of your allowed papers. Handwriting and prints are both accepted. Please see further explanations in the file below '2025/2026_exam_rules'.
  
• You can bring a calculator and a ruler
• At the end of the exam, all papers including the exam, notes, and scrap paper must be handed in together. Please note that notes and scrap paper will not be graded.
  

• http://zeiss-campus.magnet.fsu.edu/tutorials/index.html
  
• http://microscopyu.com/tutorials/
  
• http://infoscience.epfl.ch/record/201787/
  

In case of technical problems with access to course files: 

There is a workaround to avoid this error. If you right click on the file and choose "open in a new tab", then click on the file in the new tab, you shouldn't have the error.

Lecture 1: Introduction & Ray Optics 1

Lecture 2:  Ray Optics-2 & Matrix Optics-1

Lecture 3: Matrix Optics-2

Lecture 4: Matrix Optics-3 & Microscopy Design-1

Lecture 5: Microscopy Design - 2

Lecture 6: Microscopy Design - 3 & Resolution -1

Lecture 7: Resolution-2 (Interference & Diffraction)

Lecture 8: Resolution-3 (Fourier Optics & Microscopy)

Lecture 9:

Contrast and Fluorescence -1

Lecture 10: 

Fluorescence Microscopy

Lecture 11: 

Light sources in microscopy

Lecture 12:

Light Sources in Microscopy 

Fluorescence Microscopy - Filters

Lecture 13: 

Filters in optical & fluorescence microscopy

Optical detectors in microscopy

Lecture 14:

Application Examples in Biomicroscopy