Academic Courses

Academic Microscopy Courses in Israel
  • The following list is partial and is being updated constantly. All suggestions and/or additions are always welcomed.
Bar-Ilan University:
  Course Title:                      ''Advanced Optical Microscopy''
Lecturer: Prof. Yuval Garini \ Department of Physics & Nanotechnology Institute
Syllabus: Optical detection methods are intensively used in the life sciences. Starting from the simple yet powerful microscope invented ~400 years ago, optical methods, and optical imaging methods are constantly developed.

Advanced optical methods provide tools for observing objects with high spatial resolution, high spectral resolution and high sensitivity. These methods are based on pure optical effects as well as effects that involve photon-matter interaction.

The course will cover a significant number of the most important methods in optical imaging and microscopy that are used in the life sciences and biophysics. The course will start with a review of the fundamental physics required for the understanding of imaging and microscopy methods and will continue with a study of the more important methods.

The aim of the course is to provide on one hand a solid physical background to these optical microscopy methods, and on the other hand to understand the importance, capabilities and limitations of these methods.

The course will take place for one semester (two quarters), 2 hours a week (14 weeks). The course will start with review lectures and will follow with seminars on various topics prepared and presented by the students (complemented by a review on the subject). Along the course, there will be few literature study sessions. In each study, a paper will be studied and discussed. This will require preparation of the literature in advance.

Evaluation method: Home projects: 40%, Seminar presentation and preparation: 20%, Final exam: 40% (may be modified).


  1. Electric fields in matter [overview]
  2. Maxwell’s equations in vacuum & matter
  3. Diffraction theory of light
  4. Point spread function & Optical Transfer function
  5. Filtering methods (phase-contrast, Nomarski, etc.)
  6. Optical detection systems, CCD’s, PMT
  7. Introduction to fluorescence microscopy
  8. Fluorescence Resonance Energy Transfer
  9. Surface Plasmon Resonance imaging
  10. Confocal Microscopy
  11. 4pi microscopy
  12. n-photon microscopy
  13. Near-field microscopy
  14. Fluorescence Correlation Spectroscopy
  15. Advanced fluorescent molecules: quantum-dots
  16. Fluorescent Proteins, molecular beacons
  17. Spectral Imaging & Multicolor FISH
  18. I5M microscopy
  19. Saturation Depletion Microscopy
Webpage: weblink
Ben-Gurion University of the Negev:
  Course Title:                      ''Introduction to Electron Microscopy for Natural Sciences''
Lecturer: Dr. Maya Bar Sadan \ Department of Chemistry
Syllabus: The course focuses on various electron microscopy techniques. The course is intended for students from the Natural Sciences Faculty lacking previous knowledge of electron microscopy. The course may also serve as the theoretical background required for the practical courses. The goal is to introduce the operation and function of electron microscopes, the different information offered by each of them and their possible contribution for research.

  1. Introduction to Solid state
  2. Diffraction
  3. Electron Microscopy
    1. Transmission electron microscopy: Introduction and principles
      1. Electron sources and electron guns
      2. Electromagnetic lenses
      3. Resolution and limiting factors
      4. Imaging and contrast formation mechanisms
      5. The contrast transfer function
      6. Sample preparation, Vacuum systems, CCD cameras
    2. Scanning transmission electron microscopy (STEM)
    3. Analysis (STEM/TEM) – DF/BF
    4. Scanning electron microscope (SEM)
  4. Advanced topics.
  Course Title:                      ''Introduction to Electron Microscopy''
Lecturer: Dr. Louisa Meshi \ Department of Materials Engieering
Syllabus: the module intends to provide basic knowledge on electron microscopy as a science and as a technique. Upon successful completion of the module – the students will understand transmission and scanning electron microscope components, use and sample preparation. One of the major goals is that student will be able to choose an appopreate technique (among electron microscopy techniques taught) for solution of materials engineering problems and know how to prepare a sample and interpret the results.
Learning outcomes of the module: On successful completion of the course, the student should be able to:

  1. define advantages and disadvantages of transmission electron microscopy (TEM) and scanning electron microscopy (SEM) methods;
  2. list known artifacts which appear due to unappropriate sample preparation;
  3. choose appropriate SEM/TEM sample preparation technique;
  4. summarise principles of SEM, TEM and scanning –transmission (STEM) set-ups: vacuum system, detectors, scanning coils, electro-magnetic lenses, apertures, stages/holders and electron guns;
  5. define terms such as resolution of these microscopes, magnification, depth of field and depth of focus and relate influence of various factors on these terms;
  6. conlude contrast mechanisms in studied electron microscopes;
  7. describe special techniques such as HRTEM, HRSEM, cryo TEM and ESEM;
  8. differentiate among different electorn diffraction methods;
  9. index polycrystalline and single crystalline electron diffraction patterns;
  10. explain EDS and WDS methods, choose appropriate one for solution of analytical problems in material science
Remarks: The course is given on fall semesters.
  Course Title:                      ''Advanced Methods for Characterization of Structural Defects''
Lecturer: Dr. Louisa Meshi \ Department of Materials Engieering
Syllabus: the module provides tools and knowledge for successful characterization of structural defects using traditional and novel techniques of electron microscopy and X-ray diffraction. The major aim of the course to deepen the knowledge of the two methods mentioned above and to be able to choose the appropriate technique for defect characterization.
Learning outcomes of the module: On successful completion of the course, the student should be able to:
1. define advantages and disadvantages of transmission electron microscopy (TEM) and X-ray diffraction methods;
2. characterize the structure and identify phases;
3. define influence of structural defects on X-ray diffractogram;
4. calculate and identify the defects using X-ray diffraction;
5. identify the course for X-ray diffraction peak broadening;
6. define and understand the methods for 3D defect chartacterization by TEM (defects such as stacking faults, precipitates, twin and other boundaries);
7. define and understand the methods for 2D defect chartacterization by TEM (defects such as dislocations);
8. construct superimposed stereographic projection for analysis of precipitate/matrix orientation relationship
Remarks: The course is given on fall semesters.
  Course Title:                      ''Introduction to Microscopy – Basic Principles and Cryo Applications''
Lecturer: Prof. Oren Regev \ Department of Chemical Engineering
Syllabus: The student will be familiar with few electron microscopy techniques, focusing on cryo-TEM. During the course there will be lecture sessions, which will include theoretical aspects of microscopy. Demonstrations of the techniques/equipment and hands-on personal experience will be given as well.
The course is aimed at introducing the techniques and explore the possibilities in microscopy. Nevertheless, in order to operate such sophisticated equipment one will need additional long technical training period.

Introduction to Transmission Electron Microscopy (TEM)
Electron Guns

Scattering – Elastic and inelastic
Contrast transfer function
Resolution contrast and magnification

Image formation – contrast mechanisms
Electron crystallography (Ext.)
Tomography (Ext.)
Analytical methods (Ext.)
Cryogenic TEM techniques
CTF, real and reverse space

Image analysis
Microscopic imaging of colloidal particles and liquid crystalline phases.


Room temperature TEM
Imaging – CCD basics
Cryo-TEM preparation
Cryo-TEM imaging

  Course Title:                      ''Data science in cell imaging''
Lecturer: Dr. Assaf Zaritsky \ Department of Software & Information Systems Engineering​
Syllabus: The recent explosion in high-content, dynamic and multidimensional imaging data is transforming cell imaging into a “Data Science” field. This course will review the state-of-the-art in visualizing, processing, integrating and mining massive cell image data sets, deciphering complex patterns and turning them into new biological insight. It will include a mix of approaches in machine learning and computer vision (e.g., deep learning) applied to bio-imaging data.
The course is open for all ISE and adjacent departments (e.g., CS, EE) graduate and undergraduate students in their 3rd or 4th year. Interested students from other departments should contact Assaf (
The lectures will be held in English.
Background in mathematics and programming is required. No prior biological knowledge is required; all background will be covered in the lectures. Prior knowledge in machine learning and/or computer vision is highly recommended, but not necessary.
Grade will be determined by single student presentation of an academic paper (20%) and a 1-2 students semester-long project (80%).

Main topics covered in the course:
• Bioimage informatics
• High content single cell phenotypic profiling
• Quantifying cell motility: from the intraceullular to the multicellular scales
• Classifying cell state with deep learning
• Generative models for cell structure with deep learning
• Enhancing cell image quality with deep learning
• Quantifying causality with fluctuations analysis (without perturbations)
• Molecular and cellular heterogeneity
• Public data repositories, data harmonization, integration and fusion
• Importing ideas from systems biology

Webpage: weblink
Remarks: People from diverse backgrounds (Bio/Physics/Engineering/Med) are encouraged to participate. Feel free to make contact directly if you have any questions regarding the course.

Technion – Israel Institute of Technology:
  Course Title:                      ''Electron Microscopy of Soft Materials''
Lecturer: Prof. Ishi Talmon \ Chemical Engineering
Syllabus: The course provides the theoretical background for electron microscopy of liquid and semi-liquid material systems, namely, complex liquids. The course describes the operational principles the transmission- and scanning electron microscopes (TEM and SEM), their components, including electron guns, electromagnetic lenses, and detectors. The principles of image formation and electron diffraction in the TEM, and picture formation in the SEM are explained. Also described are the interactions between the electron beam and the specimen. The course emphasizes cryogenic-temperature electron microscopy methodologies, including specimen preparation, and imaging low-image-contrast, high-beam-sensitivity systems. Two laboratory-demonstrations are given in addition to the lectures.
After completing the course the student should have good understanding of electron microscopy of soft materials, its advantages, possible applications, and limitations.
Remarks: The course is given on fall semesters.
  Course Title:                      ''Analytical Scanning Electron Microscopy''
Lecturer: Dr. Alex Berner \ Materials Science & Engineering
Webpage: weblink
Remarks: The course is given on fall semesters.
  Course Title:                      ''Transmission Electron Microscopy in Materials Science''
Lecturer: Dr. Yaron Kauffmann \ Materials Science & Engineering
Syllabus: Transmission electron microscopy (TEM) is becoming more and more essential in many fields of research involving nano-scale structures. The goal of this course is to provide the student with a basis upon which s/he can interpret electron microscopy results, understand the microscopy of others, and to know when (and when not) to turn to electron microscopy for answers concerning the microstructure of materials. This course attempts to cover the basic topics required in all current microscopy techniques in use, and to delve into some of the more advanced techniques which are used in Materials Science.
Webpage: weblink
Remarks: The course is given on spring semesters.
  Course Title:                      ''In-Vivo Imaging: Theory and Practice''
Lecturer: Dr. Edith Suss-Toby \ Bioimaging Center, Biomedical Core Facility
Syllabus: Theoretical and applicative aspects of in-vivo multimodality imaging including basic principles of fluorescence and luminescence signals, ultrasound, X-Ray, CT, anatomical and functional MRI. Image analysis tools enabling 3D volumetric measurements, co-registration, nanoparticle detection and metastasis quantification.
  Course Title:                      ''Applied Microscopy''
Lecturer: Dr. Edith Suss-Toby \ Bioimaging Center, Biomedical Core Facility
Syllabus: Transmitted light microscopy, alignment and different contrast methods: Phase, DIC. Fluorescence microscopy: Excitation and emission paths, fluorescence Filters. Confocal microscopy: Laser excitation, pinhole, detectors: Cameras, PMTs. Acquisition/analysis software, signal digitization, segmentation and quantification.
Tel-Aviv University:
  Course Title:                      ''Scanning Electron Microscopy''
Lecturer: Dr. Zahava Barkay \ Wolfson Applied Materials Research Centre
Syllabus: Background to scanning electron microscopy (SEM). Electron-specimen interaction: models for elastic and inelastic interaction. Monte-Carlo simulation for electron-specimen interaction. Properties of main signals and X-ray microanalysis. Electron optics: electron sources, magnetic lenses and aberrations. Principles of image formation. Various SEM types including ESEM and advanced methods. Practical SEM aspects and various applications.
Webpage: weblink
Remarks: The course is given on fall semesters.
  Course Title:                      ''Laboratory in Scanning Electron Microscopy''
Lecturer: Dr. Zahava Barkay \ Wolfson Applied Materials Research Centre
Syllabus: The laboratory includes operation of a scanning electron microscope (SEM) and performing experiments according to the course. Sample preparation and working principles using high vacuum SEM. Practical study of operation modes and various applications. Practice of SEM operation, choice of experimental parameters and corresponding images using various detectors. Comparison with low vacuum SEM.
EDS microanalysis: spectrum accumulation and analysis, effect of working parameters on the results, element mapping.
Webpage: weblink
Remarks: The course is given on fall semesters.
  Course Title:                      ''Transmission Electron Microscopy in Materials Science''
Lecturer: Prof. Amit Kohn \ Department of Materials Science and Engineering
Syllabus: Introduction; Electron optics (electron sources, electrostatic and electromagnetic lenses, detectors), components of the microscope; Aberrations and definition of spatial resolution; Electron diffraction – SAED, micro-diffraction, CBED (basic); Imaging contrast mechanisms: mass-thickness, diffraction; Contrast transfer function of the microscope and Modulation transfer function of the detectors; Phase (high-resolution) contrast; Aberration correction and implications to phase contrast imaging; sample preparation; Time permitting: Introductory survey of analytical TEM
Remarks: The course is given on fall semesters; elective undergraduate course open to graduate.
  Course Title:                      ''Analytical Transmission Electron Microscopy for Characterization of Materials''
Lecturer: Prof. Amit Kohn \ Department of Materials Science and Engineering
Syllabus: Analytical methods in transmission electron microscopy (TEM) and scanning TEM. Analytical methods for characterizing the composition, structure, chemical bonding / electronic structure, electrostatic and magnetic fields, all at lateral resolutions ranging from nanometer scale to atomic-scale:
• Scanning TEM:
Configuration, Reciprocity theory
Z-contrast, High angle annular dark field: Contrast mechanisms, Contrast transfer function (comparison to TEM),
Aberration correction
• Spectroscopy: Physical background, lateral and energy resolution, data analysis methods for determining the composition and characterizing chemical bonding / electronic structure.
Electron Energy loss spectroscopy; Energy filtered TEM
Energy Dispersive X-ray Spectroscopy
• Mid resolution phase microscopy for mapping electrostatic and magnetic fields.
Electron holography
Differential Phase Contrast STEM
Remarks: The course is given on spring semesters; elective graduate course; followed by lab work.

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