Welcome to the

Course on Computers in Microscopy

Royal Microscopical Society

University of Cambridge

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21-25 September 1997

For details of the associated Exhibition, please click here

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

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 (optional), organised in the form of a colloquium, will offer a unique opportunity to discover some of the latest advances in this fast-moving subject. Early registration is strongly recommended.

Programme for Monday | Tuesday | Wednesday | Thursday (Colloquium)

Monday 22 September

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

10.40    Coffee

11.00    Practical Session 1

13.00    Lunch break

14.00    Course photograph (in courtyard adjacent to LT0)

14.10    Image storage and hardcopy
15.00    Fundamentals of image processing II

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 23rd September

09.00    Fundamentals of image analysis
10.00    Scientific imaging systems: video sources and image acquisition

10.40    Coffee

11.00    Practical Session 2

13.00    Lunch break

14.00    Image processing: essential tools
15.00    Computer-assisted photogrammetry

15.45    Tea

16.00    Practical Session 4

19.30    Wine Reception (hosted by Synoptics and Imaging Associates)

20.00    Course Dinner (St Catharine's)

Wednesday 24th September

09.00    Morphological techniques for image analysis
10.00    Measurements from images

10.40    Coffee

11.00    Practical Session 5

13.00    Lunch break

14.00    Computers in confocal microscopy
14.50    Image processing and reconstruction TEM

15.45    Tea

16.00    Review of Course and Discussion

16.15    Practical Session 6

19.30    Dinner (for those staying in St Catharine's)

Day Four

Click Here for details of the Colloquium on Computers in Microscopy

The colloquium is intended to cover recent progress made in the use of computers for the assessment, interpretation, restoration and enhancement of microscopical images. Of particular interest will be contributions concerning new approaches and techniques, including, but not limited to, 3D measurements and profiling, wavelets and fractals. It is hoped that papers will cover some of the comparatively new fields of application, including multi-channel imaging, instrumental control and remote microscopy.

Instructors on the course will comprise: Dr D M Holburn, Department of Engineering, University of Cambridge; Dr W O Saxton, Department of Materials Science and Metallurgy, University of Cambridge, and a small team of experts in specialist fields, who will be drawn from industry and academia.

Aims of the Course
Computers in Microscopy is a three/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 three days of the course, a combination of foundation material and more specific topics will be covered both in lectures and in practical sessions. A fourth day, which is optional, will consist of a research colloquium also entitled Computers in Microscopy, in which a number of the most recent developments will be reviewed.

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 1415 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 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. Although each participant will be offered a chance to take part in all the various activities, 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, followed by an illustrated lecture on a topic of general interest. This lecture will also be open to those not attending the course.

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. 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. Delegates will be accommodated at St Catharine's College, close to the city centre and the Department of Engineering.


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:- Dr N White, Department of Plant Sciences, University of Oxford; Dr Evelyn Gray, Department of Physiology, University of Edinburgh, Dr P Atkin, Synoptics Ltd, Cambridge.

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This page was prepared by David Holburn, and comes to you courtesy of Cambridge University Engineering Department. Last updated on 20th September 1997. 

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