The Royal Microscopical Society
Colloquium on Computers in Microscopy

Co-sponsored by the Institution of Electrical Engineers
Professional Group E4 (Image Processing and Vision)

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25th September 1997, Cambridge

For details of the associated Exhibition, open to all University members,
please click here

A Colloquium on aspects of the application of computers to microscopes and microscopical techniques was held in the University Engineering Department, Trumpington Street, Cambridge, on Thursday 25th September 1997. This colloquium was organised in collaboration with the Royal Microscopical Society, with co-sponsorship from Professional Group E4 (Image Processing and Vision) of the Institution of Electrical Engineers

The colloquium covered recent progress made in the use of computers for the assessment, interpretation, restoration and enhancement of microscopical images, including, but not restricted to applications in optical and all kinds of electron microscopy. It included contributions concerning new approaches and techniques involving automation of microscope function, 3D measurements, profiling, and digital processing techniques including wavelets and fractals. Papers were  contributed by some of the foremost laboratories, institutions and organisations working in the field, with topics covered including some of the comparatively new fields of application, including multi-channel imaging, instrumental control and remote microscopy.  A schedule is shown below, and local information is also given.  A total of twenty three delegates registered for the colloquium; a number of additional local staff attended the exhibition or a single presentation.

A small exhibition of products and materials by local organisations involved in this area was held in association with this event. Visits were organised to laboratories in the University engaged in this kind of work.

Registration details
Information for authors

The Colloquium took place immediately after a three-day course, also entitled Computers in Microscopy, and the two events were to some extent complementary, although,as expected, several delegates attending the colloquium had not attended the course. Further information about the course on Computers in Microscopy is available from the Royal Microscopical Society, or on the Web.

Click here to see details of the Course on Computers in Microscopy

Schedule and Abstracts

Important.  Please click here to see Copyright Notice.

09.15 Registration and Coffee

09.35 Welcome and Introduction
David Holburn, Chairman

09.40 Computer controlled manipulation of matter at the nanometre scale with the scanning probe microscope
M E Welland and E T Roller, Nanoscale Science Group
Department of Engineering, 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.

10.05 The Remote Microscope: Sharing information over the Internet
B C Breton, Scientific Imaging Group,
Department of Engineering, University of Cambridge
The Internet explosion is a direct result of a project at CERN, headed up by Tim Berners-Lee, to facilitate the transfer of text and graphics information amongst colleagues. The result was HTML (Hyper Text Markup Language), and thus the "Browser" was born, Internet Explorer and Netscape Navigator to name but two. Using this technology our group initiated a project 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.

10.30 Coffee, Poster Session and Exhibition

11.00 The Intelligent Microscope: Case studies of SEM fault diagnosis and control
N H M Caldwell, B C Breton and D M Holburn, Scientific Imaging Group
Department of Engineering, University of Cambridge
Thirty years of industrial development have transformed the scanning electron microscope (SEM) into a fully software-driven computer-controlled instrument. Meanwhile manufacturers incur high costs in ensuring effective instrument maintenance and the expertise level of the average SEM operator continues to diminish. Expert system technology offers an opportunity to capture diagnostic and operational expertise for inclusion in software to assist service engineers and to fully automate SEM operation. This paper will gently introduce expert system technology, and describe the design and implementation of two expert systems for electron microscopy. Some suggestions for future applications of this technology in the broader microscopy world will be given.

11.25 Resolution doubling by aperture-synthesis TEM
W O Saxton and A I Kirkland
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 paper presents some early results obtained by the approach, and outlines the experimental procedure and the computer processing required.

11.50 New approaches to image data compression for microscopy
G Chand, LEO Electron Microscopy Ltd
It is necessary to keep image data size down in order to make full use of limited storage space and network bandwidth. Lossy image compression techniques allow compression ratios far greater than those permitted by conventional lossless techniques. The talk will examine three lossy compression techniques in a microscopy context: JPEG, Fractal compression and Wavelet compression.

12.15 Automated rapid differential enumeration of microorganisms in fluorescence microscopy
T.M. Sheen1, A.R. Allen1, B. Seddon2
Department of Engineering, University of Aberdeen, Aberdeen, AB9 3UE
2Department of Agriculture, University of Aberdeen, Aberdeen, AB9 3UE
Reliable methods of rapid enumeration of microbial contamination in food samples would be a major advantage in food safety. The Direct Epifluorescent Filter Technique (DEFT) is an enumeration method with several desirable properties; it is rapid, sensitive and allows direct observation of stained microorganisms for descrimination discriminative.

This paper describes a novel combination of image processing techniques which have been developed to automate the analysis of DEFT images of micro-organisms using the Viablue-2 stain. Classification is carried out in several stages, The Canny edge detector, followed by a morphological filter is used to generate an initial image segmentation, this segmentation is then improved with a fast region merging algorithm. Boundary analysis is then used to classify the regionsinto families of micro-organisms and debris. Finally, region colour isused to classify organism viability. The software runs on a standard PC. However, in order to produce a system which operates in real time a combination of parallel processing and custom hardware has also been used to implement the algorithms. Initial results have shown increased reliability over an existing comercially available image analyzer. Further evaluation of the system is currently ongoing.

12.40 Lunch, Poster Session and Exhibition

14.10 How big is a blood vessel?
E Gray, Department of Pathology, University of Edinburgh
A computerised microscope provides an ideal enviroment for simple interactive morphometrical procedures on cells, tissues, etc in routine and research laboratories. The development of the AxioHOME, where computer graphics and text are projected into the microscope eyepieces over the sample, allows tissue specific measurement protocols to be easily constructed and carried out. The system permits simple measurements, i.e. point counting, length and area to be combined to generate a large volume of data from two dimensional specimens. The excellent X-Y relocation facilities allows the implementation of destain-restain procedures, where features of interest can be assessed for different characteristics or using different programs, i.e. morphometry and ploidy analysis. This presentation will discuss some of the research applications of the system in Edinburgh.

14.35 New image processing techniques for increased depth of field imaging for optical microscopy.
R Town, Synoptics Ltd, Cambridge
Obtaining fully focused images of samples with a large depth of field using optical microscopes is now easy to achieve using image processing techniques and without modifying the microscope. A software solution has been developed allowing users of microscopes equipped with a camera and framegrabber to obtain high quality images from even the most difficult of samples. Several examples will be demonstrated.

15.00 3-D fluorescence microscopy: a quantitative tool?
N White, Department of Plant Sciences, University of Oxford
This presentation will cover recent work at Oxford on 3-D and 4-D microscopy of intact plant and animal tissues, including some new developments in laser scanning microscopy and digital microscopy. The aim will be to show, in practical terms, how to make multidimensional microscopy a quantitative tool and to describe the current state of progress in these areas.

15.25 Correction and quantification of CLSM volumes using deconvolution and segmentation
C Daly, D Luo & J C McGrath, University of Glasgow, Glasgow
Laser scanning confocal microscopy (LSCM) can be used to study 3-D structure of blood vessels by image analysis and pattern recognition. However, laser blurring cased by the reflection and refraction of light inside the objects and on the medium boundary can lead to inaccurate measurements and loss of vital information. To overcome this problem for vascular tissue, we have tested a variety of deconvolution methods for image restoration.  Wiener Filter (WF), Iterative Tikhonov-Miller (ITM) restoration, or Iterative Maximum Likelihood Estimation (IMLE) restoration was then used to deconvolve the blurred image (original data).  Experiments using the three deconvolution methods suggest that ITM and IMLE produce more satisfactory restoration but runs slower than WF, depending on the number of iterations.

We have now extended these studies using automated image analysis and pattern recognition. A fully automated multi-threshold method for image segmentation has been developed; experiments have shown this method to give good segmentation and separation, enabling multiple objects in a single image to be segmented at different values.   This method has been used in the determination of the elastin network in 10 mm cross sections of rat thoracic aorta and in studies of vascular cell arrangement using nuclear stains. After smoothing and edge detection, the segmentation process produced significantly improved 3D images of elastin lamina or nuclei.

15.50 Tea and Poster Session

16.05 Digital Imaging of Optical Probes
W O'Brien, Life Science Resources Ltd, Cambridge
Recent years have seen an explosion in the use of optical probes for biological activity. As these probes have entered into more widespread use, the technologies for studying them using quantitative microscopy and imaging have evolved at a rapid pace as well. This talk will discuss quantitative approaches to the use of various optical probes in living cells for measuring biological parameters as diverse as calcium concentration, pH, membrane potential and genetic activity. The technology of cooled digital CCD imaging systems has given scientists previously impossible insights into the inner workings of living cells, allowing accurate, reproducible and sensitive measurements to be made without perturbing the normal function of these systems. The talk will be illustrated with examples of advances made that would have been impossible without the contribution of imaging technologies.

16.30 End of Colloquium. Optional Laboratory visits

Poster Session
Contributions promised so far include:-

Characterisation and cellular localisation of alpha 1-adrenoreceptors using LSCM
J F MacKenzie, C J Daly, D Luo & J C McGrath, University of Glasgow, Glasgow
High affinity fluorescent ligands based on "antagonist" drugs/ligands can be used like radioligands and their specificity can be verified in competition binding experiments using confocal laser scanning microscopy (CLSM) and image analysis methods. A fluorescent quinazoline derivative, QAPB was shown to retain high affinity for, and act as a non-selective competitive antagonist at, a1-adrenoceptors on fibroblasts transfected with the recombinant human adrenoreceptor subtypes a1a, a1b and a1d. Fluorescent competitive binding properties in the same cells with non-fluorescent selective ligands were found to be comparable to radioligand binding. In addition, this method offers several advantages unattainable by radioligands. 3D image analysis localised fluorescence on both the cell surface membrane and subcellular compartments within live cells. Furthermore, temporal resolution was attained and binding followed in real time in live cells with the consequent advantages of studying the kinetic properties of the receptors and their relationship to cellular activation processes. This approach should have widespread applicability in non-radioactive assays determining the location, quantity and binding properties of receptors and other biological molecules on live tissue.

3-D object reconstruction and measurement from laser scanning confocal microscopy images
D Luo, C Daly, A Robert, S Arribas, J F MacKenzie, S McGrory & J C McGrath, University of Glasgow, Glasgow
LSCM methods have been used to visualise blood vessel structure (Arribas 1994). However, automated methods for 3-D structural analysis (i.e. measurement) are not widely available.  We have developed a method of 3-D object reconstruction of LSCM images by a slice merging method. This method classifies two connected object slices in two adjacent image planes as representing a single object, otherwise they are classed independently. 3-D object measurements are obtained by the principal component transform. This method transforms the length of an object into the first principal axis, width into the second axis, and thickness into the third axis. Experiments have shown that this method is effective in reconstructing and measuring 3-D objects from LSCM images. The method has been applied to studies of vascular cell arrangement using nuclear stains, and in the determination of elastin network in 10 mm cross section of rat thoracic aorta using specific elastin stains (Weigert).

A closely integrated reconfigurable image capture device for embedded applications
D S Jordan and D M Holburn, Scientific Imaging Group
Department of Engineering, University of Cambridge
A modular digital image capture sysem has been developed which closely integrates a CCD sensor, image capture and image processing. The aim is to produce a single compact unit combining the functionality of a complete image capture and processing system. One of the benefits of the close integration is to give a direct mapping between elements in the CCD sensor and pixels in the digital image, giving greater accuracy in measurement applications. Other benefits include possible closed loop control of image acquisition and sensor parameters, reduction of output data bandwidth by local image processing and analysis, and flexible CCD sensor parameters as a standard video signal with defined, fixed parameters is not necessary. A highly compact form of the image capture system is in an advanced stage of development, using just two chips, a FPGA and a VRAM.

A separate development using a novel modular interconnection technique, has produced a miniature compact PC highly suited to integration with the compact image capture system. The interconnection technique consists of two components; a carrier for VLSI circuits and a connector to interconnect the VLSI carriers. A system consists of a number of carriers and connectors stack together in a tower-like structure. The connectors may be easily taken apart and either additional
carriers added or new carriers substituted. This allows the system to be reconfigured for different applications and to be upgraded to take advantage of technological advances without the need to redesign the whole system. The miniature PC consists of five different carriers. Work is under way to interface the compact capture system to the PC using this interconnection technique, combining CCD sensor, image capture and image processing into a single reconfigurable compact unit.

1997 Royal Microscopical Society.   Authorization to reproduce abstracts for uses other than personal or internal use should be addressed to the Royal Microscopical Society.

Information for authors and delegates
For further information about the colloquium, please contact:-

D M Holburn, University Engineering Department, Trumpington Street, Cambridge CB2 1PZ, U.K.

Telephone number:- +44 (1223) 332775.

Registration details

Fee for registration at the Colloquium 50.00
(includes admission, set of abstracts, tea, coffee and biscuits)

Buffet lunch tickets 6.00
(limited numbers available) 

If you wish to reserve a lunch ticket, please email David Holburn

For further registration details, or to request a registration form, please contact:-
Rebecca Morden
The Royal Microscopical Society
37/38 St Clements
Oxford OX4 1AJ

PHONE: +44 (0) 1865 248768
FAX:+44 (0) 1865 791237

Electronic Mail:

Colloquium facilities
Lecture room facilities include:-

Local Information

Click here for a map showing the local approaches to the Engineering Department.

Click here for tourist information about the Cambridge area.

Accommodation can be arranged in St Catharine's College, Cambridge, which is a short walk from the Colloquium venue. Dinner, bed and breakfast or bed and breakfast only can be provided. For details, please contact Rebecca Morden at RMS.

Please do not contact St Catharine's College direct.

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