Introductory description

This module provides a foundation in the principles and applications of microscopy, starting with basics of light microscopy and progressing to state of the art confocal microscopy, electron microscopy and scanned probe microscopy. The latter includes atomic force microscopy and electrochemical imaging techniques for which Warwick is particularly well-known. The module includes workshops on image analysis and seminars that cover the most recent developments in the field.

Module web page

Module aims

Outline syllabus

This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.

1. Outline Syllabus
   The focus is on high resolution techniques (spatial and time) capable of providing new insights into the structure and function of biomolecules and biomolecular assemblies (artificial systems and living cells). Recent advances in powerful new microscopy techniques will receive particular attention. For each technique considered, basic principles and theory, instrumentation, experimental considerations and sample preparation will be covered. (The structure of the course is designed in a modular way such that it is possible for other researchers to attend specific parts.) Topics will include:

• Light microscopy: Principles of light microscopy with an emphasis on fluorescence microscopy. Super-resolution techniques. Live cell imaging. Force measurements.
• Image Processing: Introduction to digital image processing with ImageJ, Convolutions and filtering, Working with colour images, Working with time-series, Filtering in frequency space, Deconvolution.
• Atomic force microscopy (AFM): Intermolecular forces, imaging techniques (contact versus tapping mode), force curve analysis: ligand-receptor binding, elasticity measurements.
• Scanning tunnelling microscopy (STM): Atomic level imaging, scanning tunnelling spectroscopy (STS) and conductivity measurements, electrochemical STM.
• Electrochemical Scanned Probe Microscopy (Scanning electrochemical microscopy (SECM) and Scanning Ion Conductance Microscopy (SICM): Theory of transport and diffusion phenomena , imaging, probing surface reactivity (e.g. immobilised enzyme kinetics, membrane transport, lateral diffusion in membranes), ion channel activity, smart patch clamping., signalling in cell assemblies.
• Cryo electron microscopy: Review of electron microscopy, advantages, disadvantages, applications.

Learning outcomes

By the end of the module, students should be able to:

• (a) Subject knowledge and understanding: Understand imaging techniques and their application in structural and chemical characterisation of cellular dynamics, biophysical and materials systems on a wide range of length scales and environments. What signal the instrument produces and how that is transformed into the output the user receives. How the instrument output is used to deduce information, particularly on structure, properties and dynamics. How to improve signal:noise, sample environment and resolution (space and time). How images are formed and methods for their quantitative analysis.
• (b) Key Skills: Know how a wide range of different types of microscopes work. Know how to prepare samples and collect data for each technique studied. Know how to analyse data from each technique. Know how to use the data to deduce structure, interactions, and dynamics.
• (c) Cognitive Skills: The key challenge for this module is for mathematical scientists to be able to collect experimental data and for physical scientists to understand the mathematical processes of data manipulation.
• (d) Subject-Specific/Professional Skills: Faced with a new problem, students will be capable of choosing the most appropriate method and be able to analyse data and understand the type of information that the technique provides.

Indicative reading list

Illustrative Biography

1. Fundamentals of Light Microscopy and Electronic Imaging, 2nd edition, DB Murphy, MW Davidson, Wiley-Blackwell.
2. Atomic Force Microscopy for Biologists, VJ Morris, AR Kirby, AP Gunning, Imperial College Press.
3. Scanning Probe Microscopy and Spectroscopy: Theory, Techniques, and Applications, D Bonnell, Wiley-VCH.Confocal Laser Scanning Microscopy, CJR Sheppard, DM Hotton, D Shotton, Springer-Verlag.
4. Scanning Electrochemical Microscopy, AJ Bard and MV Mirkin, Marcel Dekker.
5. The Image Processing Handbook, John C. Russ, CRC Press.
6. Handbook of biological confocal microscopy. 3rd edition. James Pawley (Editor). Springer, 2006.

in addition to a range of recent methods publications that are the basis for the News&Views assignment.

Interdisciplinary

Students learn how to use physical methods and mathematical image manipulation to understand biological systems.

Subject specific skills

Subject knowledge and understanding:

• Understand the range of microscopy techniques that can be used in characterisation of surfaces, interfaces, cells, molecules and materials.
• Understand the construction and operation of a wide range of microscopes and the origin of measured signal.
• Know what signal the microscope produces and how that is transformed into the image the user receives.
• Understand how to analyse and derive information from images
  Key Skills
• Ability to write reports on work undertaken.
• Ability to present the results of frontier research as a short article for a general scientific audience.
  Cognitive Skills:
• The key challenge for this module is for mathematical scientists to be able to analyse experimental imaging data and for life scientists to understand the mathematical processes of image analysis.
  Subject-Specific/Professional Skills:
• Know how to prepare samples and collect data for each microscopy technique studied.
• Know how to analyse data from each technique.
• Know how to use the data to deduce information about surfaces, interfaces, molecules and materials.
• Understand instrument output versus data file produced.

Transferable skills

Communication skills (verbal and written)
Problem solving skills
Information and digital literacy (coding)
Critical thinking