[Univ of Cambridge] [Dept of Engineering] rmsflak2.gif (2388 bytes)

Welcome to the Course on Computers in Microscopy

14 - 17 September 1998

Organised in collaboration with the Royal Microscopical Society

Exhibition of hardware & software on Wednesday 16th September
for all interested members of the University

Lectures on image processing & analysis on Thursday 17th September
open to all interested members of the University

Opportunities for manufacturers or organisations
wishing to exhibiting products or services

WWW Resource Page
for Computers in Microscopy 1998

Course Organiser: Dr D M Holburn, University Engineering Department, Trumpington Street, Cambridge.

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Click on either of the thumbnails to see the full size image ..

Over the last few years, computers and digital techniques have found increasing application in almost all areas of microscopy, ranging from computer control of instrumental functions to the presentation of the final image.

In light microscopy, video camera attachments are now widely used to allow convenient manipulation, interpretation and storage of images. In transmission electron microscopy, digital densitometry of micrographs followed by image processing is already routine in many laboratories; on-line processing using the output from a low-light-level TV camera has now emerged from the experimental stage, and offers the possibility of greater ease of adjustment and repeatability. Image analysers may now be directly coupled to the SEM, and in some cases, the SEM is managed by a powerful computer, providing a consistent and versatile user interface and the potential for advanced image processing within the instrument. Advantage is being taken of the ready availability of low-cost personal computers and software for the analysis of micrographs, diffraction patterns and for the evaluation of stereo pairs. The meteoric growth of networking and the Internet means that it is now perfectly possible to make microscopical images available across the world, in seconds, and even to operate an instrument remotely.

This three/four-day intensive course aims to provide an introduction to fundamental computer techniques applicable to microscopy, together with an up-to-date review of current practice and an exhibition of equipment currently in use in all types of microscopy. It builds upon previous sucessful course on this topic which have run successfully since 1986. Lectured material will be interspersed with practical demonstrations and hands-on experience, and will cover many of the major techniques involving the use of computers. The course will be suitable both for beginners in this area, and for users who already have some experience in applying computers. Course tutors and other experts will be available to contribute to technical discussions. Numbers on the course will be restricted in order to ensure enhanced individual attention. The fourth day will offer a further opportunity to discover some of the latest advances in this fast-moving subject. Early registration is strongly recommended.

Provisional Programme for Monday | Tuesday | Wednesday | Thursday

newtiny.gif (139 bytes)  Provisional synopses of some of the lectures are available here!

Monday 14 September

09.00    Introduction to computers in microscopy
09.10    Fundamentals of image processing I
10.00    Framestores and applications

10.45    Coffee

11.00    Practical Session 1

13.00    Lunch break

14.00    Course photograph (in courtyard adjacent to LT0)

14.10    Fundamentals of image processing II
15.05    Computers in confocal microscopy

15.45    Tea

16.00    Practical Session 2

19.30    Dinner (St Catharine's)

20.30    Computer-based tools for teaching microscopy, the World Wide Web
             (Dept. Materials Science & Metallurgy)

Tuesday 15th September

09.00   Fundamentals of image analysis
10.00   Morphological techniques for image analysis

10.45    Coffee

11.00    Practical Session 2

13.00    Lunch break

14.00    Scientific imaging systems: video sources and image acquisition
14.40    Colour imaging techniques
15.25    Image formats and conversion

15.45    Tea

16.00    Practical Session 4

20.00    Dinner (St Catharine's)

Wednesday 16th September

09.00    Image processing: essential tools
10.00    Measurements from images

10.40    Coffee

11.00    Practical Session 5

13.00    Lunch break

14.00    Image storage and hardcopy
14.30    Computer-assisted photogrammetry
15.05    Image processing and reconstruction

16.00    Tea

16.15    Review of Course and Discussion

16.30    Practical Session 6

19.30    Wine Reception (hosted by Synoptics and Carl Zeiss UK)
20.00    Course Dinner

Thursday 17th September (provisional programme) newtiny.gif (931 bytes)Please note updated timimgs!

09.00    Evolution of Telemicroscopy using the World Wide Web (B C Breton, University of Cambridge)
The Internet explosion is a direct result of a project at CERN, to facilitate the transfer of text and graphics information amongst colleagues: the result was HTML (Hyper Text Markup Language).  In 1995 our group initiated a project using this technology that allows microscopists to share information using a Scanning Electron Microscope (SEM). The SEM is connected to the Internet and can be operated remotely as well as monitoring information. The same technology allows the SEM to be operated over existing analogue telephone or the newer ISDN digital systems. The technology includes dynamic imaging which will be demonstrated.

09.30    Intelligent Microscopy (N H M Caldwell, University of Cambridge)
Thirty years of industrial development has transformed the scanning electron microscope (SEM) into a fully software-driven computer-controlled instrument. Meanwhile the expertise level of the average SEM operator continues to diminish. Expert system technology offers an opportunity to capture operational expertise for inclusion in software to assist microscopists. This presentation will gently introduce expert system technology, and describe the design and implementation of the XpertEze system. Some suggestions for future applications of this technology in the broader microscopy world will be given.

10.00    Telemicroscopy (Dr E Gray, University of Edinburgh)
This lecture will cover newly emerging techniques for remote access to optical microscopes.  It is expected to include: passive and active telemicroscopy, specifications of current available optical systems, use in biological applications.   An internet link will be established to demonstrate active use (expected to take place Wednesday p.m.)

10.20    Virtual Microscopy as a Teaching Resource (Dr L Baggott, University of Exeter)
The Interactive Microscope Laboratory (IML) is a simulation of a functional microscope on CD-ROM for use in biological education. An evaluation of the prototype CD-ROM was carried out in English secondary schools, with pupils aged 14-18. This paper describes their responses to the simulation, together with evidence of their use of Information and Communications Technology (ICT) and microscopes more generally. These are discussed in the context of the use of new multimedia technologies in school science education.

10.50-11.20    Coffee in LR 4

11.20    Computer Control for Resolution enhancement in the TEM (Dr W O Saxton, University of Cambridge)
Recent developments in computer control of TEM has made possible experimental procedures not previously feasible. One of these involves the recording of several images of a specimen with the beam tilted in different directions, from which computer Fourier synthesis allows a final image showing faithful detail at half the size of any conventional image. This lecture outlines the experimental procedure and the computer processing required, and presents some  results obtained by the approach.

11.50    Monte Carlo Simulation of Electron Trajectories (Dr E Napchan, Imperial College)
This lecture is expected to cover the following topics: elastic/inelastic scattering models,. energy loss expressions, random numbers.  Simulation procedures, data generated, verification.  Integration of simulation and experimental data, electron microscopy experiment design.  Demonstration.  Additional sources and references.

12.20    Scanning Probe Microscopy (Dr M E Welland, University of Cambridge)
By computer control of the way in which the tip of a scanning probe microscope interacts a surface it is possible to manipulate matter at the atomic level. The technique relies on sub-Angstrom control of the position of the tip and precise measurement of the way in which the tip interacts with the object to be moved. For example, in moving C60 molecules across the surface the tip needs to be positioned behind the molecule so that the predominant force acting is in a direction parallel to the surface. Motion of the molecule is effected by 'pushing' the C60 with the tip in a way analogous to pushing one billiard ball with another. In addition to simply moving matter it is also possible to measure the forces required to effect motion so that important energetic quantities relating to the mechanical properties of individual molecules can be quantified.

12.50    End of course

Programme to be confirmed

Aims of the Course
Computers in Microscopy is a four day course covering both theoretical and practical aspects of the application of computer techniques to the science of microscopy. The course provides a thorough understanding of the fundamentals of digital image acquisition, processing and analysis, including key techniques for their implementation and integration in practical, cost-effective applications for all branches of microscopy.

Throughout the course, participants will have opportunities to experiment and learn on a variety of image processing systems, and to discuss specific problems and applications with course tutors and manufacturers' technical representatives. The lectured material will be augmented with demonstrations of computers being applied to a range of practical problems, as well as opportunities for direct hands-on experience using computers and software packages assembled for the exclusive use of course participants. Manufacturers' representatives work in close collaboration with course tutors to provide relevant demonstrations and hands-on sessions using up-to-date commercial equipment. Participants will be welcome to bring to the course material related to their own profession. Facilities will be available for input of images by means of video cameras and scanners.

After attending the course, a participant will be equipped to discuss with other users the principles and relative merits of a wide range of practical techniques. Through the lectured material and the practical sessions, he or she will gain an insight into some of the important advantages that accrue from the use of computers in microscopy, as well as some of the pitfalls and misunderstandings that can arise. Moreover, participants who may intend soon to purchase or recommend computer equipment for their employers should be better placed to make an informed decision about the merits of commercially available systems.

Who should attend
The course is directed at scientists, engineers and teachers involved in the use of microscopy for any purpose (including, but not limited to, optical, transmission electron and scanning electron microscopy). Much of the material is equally applicable to the physical, materials and life sciences. The course should also be useful to teachers who wish to update their appreciation of the most up-to-date techniques, or managers who may be contemplating the acquisition of computer-based equipment for microscopy.

Course Format
The course will consist of lectures interspersed with practical sessions. Lectures are held in a hall equipped with a wide variety of audio visual aids, including networked computers, projection TV, and so on. A comprehensive set of lecture notes will be provided for all participants. For the first three days of the course, a combination of foundation material and more specific topics will be covered both in lectures and in practical sessions. The fourth day will consist of a number of sessions, some running in parallel, in which a number of the most recent developments will be reviewed.  The course will end at lunch time on the fourth day, allowing time for sight-seeing or the return journey.

Two lectures will start the day at 0900 hours. These will allow ample opportunity for introducing important fundamental concepts or theory. After a tea/coffee break, a practical session will follow, and will take place in a room adjacent to the lecture hall. This will consist of exercises to be carried out, typically alone or in pairs, on the suite of workstations provided. Demonstrators will be on hand to give expert assistance where required. Further demonstrations will be offered by manufacturers who will supervise and operate their own equipment. These will give an opportunity for participants to gain practical experience of the techniques covered in the lectures. Where appropriate, a final short lecture may serve to summarise the morning's work, or introduce a new topic. The lunch break will last from 1300 hours to 1400 hours. No specific arrangements will be made for lunch, but a number of congenial restaurants, bars and public houses lie within easy walking distance, and each participant will be provided with a map showing how to reach these.

The afternoon programme will include two/three lectures of intermediate length. These are intended to introduce more specialised topics, and will be followed by a further opportunity to participate in practical exercises, hands-on sessions, manufacturers' presentations and demonstrations, discussions with manufacturers' representatives and visits to laboratories and nearby companies.  Where necessary, the timing of the afternoon sessions may vary slightly from this format to accommodate demonstrations or lectures which cannot be given at any other time.  Each participant will be offered a chance to take part in all the various activities; however, there will be some freedom for the individual to concentrate on those activities that are perceived to be of greatest use. To allow this flexibility, the number of registrants will be restricted, and early registration is strongly recommended.

After dinner in College, a number of evening activities will be organised. These will include short lectures of a less formal nature, visits, or demonstrations of software packages. The evening will close with informal discussion, taking place either in the College bar, or in one of the many congenial bars and public houses scattered around Cambridge. On the third day, there will be a Course Dinner with wine reception.

Other Information
The course will be held at Cambridge University Engineering Department, Cambridge, England. It draws on the unique strengths of Cambridge and its surroundings as a centre of scholarship, research and commerce.  Delegates will be accommodated at St Catharine's College, close to the city centre and the Department of Engineering.

Cambridge is one of England’s oldest cities with roots going back to the Iron Age. The first Scholars arrived in Cambridge in 1209, having become disillusioned with life in Oxford. Peterhouse is the oldest of the colleges, having been founded in 1284 by the then Bishop of Ely, Hugh de Balsham. Colleges have continued to grow and now number 31, with the newest college, Robinson, having been founded in 1977. The University is acknowledged as one of the best in the world, with leading-edge research being carried out in all the major academic disciplines But there is more to Cambridge than the University - there are numerous museums and art galleries within the city, including the world famous Fitzwilliam Museum, not to mention the most successful Science Park in Europe.

Access to Cambridge by air is possible direct from Amsterdam or Manchester, and via Stansted Airport from many other continental European cities. Coach services are available from Heathrow, Gatwick and Stansted Airports. Rail communications to Cambridge are excellent.


Dr David Holburn
joined the University of Cambridge Engineering Department as a lecturer in 1986. His research interests include the development of software for applications in scanning electron microscopy, image processing and analysis, and the design of high speed integrated hardware systems for machine vision and other purposes. He is the author of the EPICplus software package for image processing and analysis.

Dr Owen Saxton joined the University of Cambridge Department of Materials Science and Metallurgy in 1983. He has spent over 20 years engaged in research in electron microscopy and software for image processing and restoration. He is a major author of the SEMPER image processing software package.

Other specialist lectures and assistant staff will participate, and will be drawn from other departments of the University, local industry, research establishments, and other universities and institutions. The list of specialist lecturers is expected to include:-

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This page was prepared by David Holburn, and comes to you courtesy of Cambridge University Engineering Department.
Last updated on 10th September 1998.