Microscopy and image analysis of biological samples - project work

Subject description

– Upgrading of student’s basic knowledge on light microscopy techniques (e.g. microscopy in a dark field, phase-contrast microscopy, interference contrast-DIC microscopy and fluorescent microscopy), their advantages and applications on biological samples

– Procedures for image acquisition, processing, and quantitative analysis of micrographs

– advanced light microscopic techniques with demonstration of optical sectioning and 3D reconstruction on biological samples

– Principles and techniques of transmission electronic microscopy (TEM) for structural analysis of biological samples (tissues, cells, bacterial, viral particles, liposomes…) with special emphasis on understanding of methodology, interpretation of micrographs and practical preparation of biological samples

– Principles and demonstration of scanning electron microscopy (SEM), its application on biological samples, interpretation of micrographs and practical approaches in sample preparation.

– Principles and examples of high resolution transmission electron microscopy (HRTEM) and spectroscopic methods (EDXS, EELS) of biological samples

– Principles of advanced microscopic techniques and approaches for visualization of biological samples

The subject is taught in programs

Objectives and competences

– upgrade of basic knowledge on microscopic methods

– acquaintance with properties (benefits and potential drawbacks) of various microscopic techniques

– acquaintance with preparation procedures of biological samples o with various microscopic techniques

– acquiring of basic skills on acquisition, processing, analysis and interpretation of images of biological samples

– development of self-initiative approach in designing of experiment, which include visualization approaches

Teaching and learning methods

Consultations, seminars (as background of individual project) and individual project

Expected study results

Knowledge and understanding:

– understanding of physical background of microscopic techniques

– choosing of appropriate microscopic approach in experiment design

– knowledge on basic procedures of biological sample preparation for light and electron microscopy

– basic knowledge on image acquisition,  processing and analysis

– ability of interpretation of micrographs depicting biological samples

Basic sources and literature

– Izbrani članki iz strokovnih revij:

– Microscopy and microanalysis online journal; Wiley and Sons

– Journal of Microscopy, Blackwell publishing

– Hayat M. A. (2000) Principles and techniques of electron microscopy – Biological applications. 4th Edition. Cambridge University Press, cambridge, UK, 543 str., ISBN 0-521-63287-0 (izbrana poglavja str. 367-388, 400-436)

– Bozzola J.J., Russell L.D. (1999): Electron microscopy – Principles and Techniques for Biologists. 2nd Edition. Jones and Bartlett Publishers, Subdury, Masachusetts, USA, 670 str., ISBN 0-7637-0192-0 (str. 16-46, 120-146, 148-201, 262-278, 368-394, 442- 475, 480-608).

– Allen T.D. (ur.) (2008) Introduction to Electron Microscopy for Biologists, Methods in Cell Biology 88, izbrana poglavja D.B. Williams, C.B. Carter, Transmission Electron Microscopy, Plenum Press, 1996, izbrana poglavja

– Russ J.C. (2011) The Image Processing Handbook, 6th Edition. CRC Press, USA, 885 str., ISBN 978-1-4398-4045-0, izbrana poglavja

Stay up to date

University of Ljubljana, Faculty of Electrical Engineering Tržaška cesta 25, 1000 Ljubljana

E:  dekanat@fe.uni-lj.si T:  01 4768 411