Biomicroscopy I

MICRO-561 / 4 credits

Teacher: Altug Hatice

Language: English

Summary

Introduction to geometrical and wave optics for understanding the principles of optical microscopes, their advantages and limitations. Describing the basic microscopy components and the commonly used biomicrocopy methods such as widefield and fluorescence.

Content

Geometrical and matrix (ABCD) optics, wave and Fourier optics, point-spread function (PSF), resolution and contrast, microscope elements (objectivs, eyepiece, filters, illuminations, detectors), fluorescence microscopy, and preparation of biological samples for microscopy.

Keywords

Optical microscopy, fluorescence, wide field microscopy.

Learning Prerequisites

Required courses

Analysis IV, Linear algebra, General physics III/IV.

Important concepts to start the course

Basic matrix calculations, Fourier transformation, electromagnetic waves, refraction and reflection.

Learning Outcomes

By the end of the course, the student must be able to:

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

Transversal skills

  • Communicate effectively with professionals from other disciplines.

Teaching methods

Lecturing with exercises.

Expected student activities

Following the lecturing and solving the exercises regularly is necessary for mastering the course contents. The solutions of the exercises are distributed at the next lecture. The student is invited to find his/her own solutions and to discuss them with the assistants.

Assessment methods

Written exam during the winter exam session

Supervision

Office hours No
Assistants Yes
Forum Yes
Others Possible to take dates.

Resources

Bibliography

¿ Fundamentals of Light Microscopy and Electronic Imaging, 2nd Edition, by Murphy and Davidson. Wiley-Blackwell (2013).

¿ Fundamentals of Photonics, 2nd Edition, by Saleh and Teich. Wiley (2007).

¿ Geometrical and matrix optics: José-Philippe Pérez, Optique: fondements et applications (2004).

¿ Eugene Hecht, Optics (2002).

¿ Miles V. Klein and Thomas E. Furtak, Optics (1986).

Ressources en bibliothèque

Notes/Handbook

Script covering geometrical and matrix optics, Fourier optics, microscopy and fluorescence. Script chapters and course slides are published on Moodle.

Websites

Moodle Link

Prerequisite for

Biomicroscopy II

In the programs

  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Exam form: Written (winter session)
  • Subject examined: Biomicroscopy I
  • Courses: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Type: optional

Reference week

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