IAfM-Booklet dr12.cwk - The University of Liverpool

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IAf M - 06

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General Information $

Contact and Travel Information (

Map of City of Liverpool )

Map of Locality of IAfM &

Building plan for D&R Hall *

Programme � Overview +

Programme � Monday "

Programme � Tuesday morning !%

Programme � Tuesday afternoon !!

Programme � Wednesday !$

Abstracts !( � ,!

List of Delegates ,$

The organisers of IAfM#%& acknowledge the generous sponsorship of the following organisations

Thin Films and Surfaces Group The University of Liverpool Surfaces of Complex Metallic Alloys

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Contact details for travel information are given on page ( and a map of the city of Liverpool showing the location of Derby and Rathbone Hall is on page )- A larger scale map of the locality of D&R Hall is on page &-

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A building plan of Derby and Rathbone Hall (page *) shows the location of the Reading Room' where registration will take place on Monday morning' and the Knowsley Room where the talks will be held- Delegates staying at D&R Hall can pick up their room keys from the Reception desk- For delegates staying at the Alicia Hotel' this is a short walk across Sefton Park (see map on page &)-

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On Monday there will be a few introductory words of welcome at $-%% pm and then the talks will start at $-!) pm-

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All speakers in a morning or afternoon session are asked to copy their presentations onto one of the Mac or PC laptops before the session starts-

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All of the talks will take place in the Knowsley Room- Refreshments will be served in the mid#morning and mid#afternoon breaks in the adjacent Reading Room' where some exhibitors will demonstrate their products- Lunches and dinners will be served in the Dining Room' close to the Reception-

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After dinner on Monday evening there will be the final talk of the day and then the bar (located above the Reception) will be open until !! pm- On Tuesday the Conference Dinner will be at * pm' early enough to placate those delegates who would like to watch the England v Sweden World Cup match (kick�off at + pm)' and again the bar will be open until !! pm-

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For those looking for local restaurants on Sunday or Wednesday evenings' and for those not taking the Conference Dinner' check the web (see next page)-

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( Aigburth Drive' Sefton Park' Liverpool L!* (AATel: %!)! *$* ,,!!http://www-feathers-uk-com/aliciaEmail: alicia@bestwestern-co-ukLocation: http://www-liv-ac-uk/.sdb/IAfM%&/Liverpool#map-pdfSee also maps on pages ) and &

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North Mossley Hill Road' Liverpool L!+ +BHTel: %!)! *", &,)! (Admin- Office)Tel: %!)! *", &,)& (Porters' Lodge)http://www-liv-ac-uk/conferenceservices/conferences/greenbank-htmTravel directions and map: http://www-liv-ac-uk/.sdb/IAfM%&/IAfM#Travel-pdfBuilding plan of D&R Hall: http://www-liv-ac-uk/.sdb/IAfM%&/DR#plan-pdfSee also maps on pages )�*

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The Knowsley Room has wireless access' the Reading Room has wired connectionsUse username �scndvyxx� (where xx / %%' %!' %$' %(' ---) and password �apt$[vow�

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http://www-liverpoolairport-comTel: %+*% !$" +,+, (for passenger information)Tel: %"%& !%+ +,+, (for all flight information including departures and arrivals)

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Train times: http://www-nationalrail-co-ukLocation: See map on page )

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http://www-manchesterairport-co-ukTel: %"% !% !% !%%% (for Flightline)Tel: %!&! ,+" (%%% (for general Manchester Airport enquiries)

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Train times: http://www-nationalrail-co-ukLocation: See maps on pages ) and &

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For information on restaurants in the locality of D&R Hall usehttp://www-sugarvine-com and search for Liverpool South

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Tel: %!)! *", &,,%Fax: %!)! *", &)$%Email: conference@liverpool-ac-uk

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Monday !,:%% Invited TalkS ScheuringInstitut Curie' Paris' FranceImage analysis of atomic force microscopy data in membrane research

Monday !):%%R I Han' A Black' AT French and B M CorcoranRoyal (Dick) School of Veterinary Studies' University of Edinburgh' UKInterstitial cells in myxomatous areas of canine mitral valves

Monday !&:%%C P Martin' P Siepman' M O Blunt' E Vaujour' N Krasnogor and P J MoriartySchool of Physics and Astronomy' University of Nottingham' UKUnderstanding nanoparticle pattern formation: Experiments' simulations' morphometry and genetic algorithms

Monday !&:(%R Hathiwala and J ChapmanOlympus' UKLive cell imaging

Monday !*:%%D Zhu' F Prin' A Gould and S N PagakisConfocal Imaging Analysis Laboratory' National Institute for Medical Research' UKQuantitation of cell sorting using morphological image analysis

Monday !*:(%J Walton and N FairleySchool of Materials' University of Manchester' UKNoise reduction in spectrum image datasets using principal component analysis

Monday !":%% Invited TalkA M NewsamAstrophysics Research Institute' Liverpool John Moores University' UKExtreme E-T-? Searching for Extra#Galactic Planets

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Tuesday ":%% Invited TalkA ThorsenInstitute of Marine Research' Bergen' NorwayUsing particle analysis to determine reproductive characteristics of fish species

Tuesday !%:%%M Safrai' D Darvish' Z Malik and A WeissDepartment of Biology' Bar Ilan University' IsraelMorphological analysis of butyrate#induced differentiation in B!& melanoma

Tuesday !!:%%R Wightman' R Marshall and S TurnerFaculty of Life Sciences' University of Manchester' UKImage processing for understanding cellulose synthesis at the plant cell surface

Tuesday !!:(%J Francis and M PrestonMedia Cybernetics' UKImage Analysis Software Suite from Media Cybernetics

Tuesday !$:%%R H Fleming and D H MurrayRoslin Institute and University of Edinburgh' UKImage analysis applied to studies of avian bone

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Tuesday !,:%% Invited TalkR HeilbronnerDepartment of Geosciences' University of Basel' SwitzerlandOrientation imaging: Measuring and mapping crystallographic orientations

Tuesday !):%%C D Barrie' A P Boyle and D J PriorDepartment of Earth and Ocean Sciences' University of Liverpool' UKThe use of image analysis in understanding microstructures in experimentally deformed pyrite

Tuesday !&:%%N G D Kouankap' S Ganno and P T AzinwiDepartment of Earth Sciences' University of Yaoundé !' CameroonNew technique in obtaining high quality photomicrographs with the help of a simple transmitted microscope and its contributions in microstructural geology and micro#petrographic studies

Tuesday !&:(% Invited TalkK L BrainDepartment of Pharmacology' University of Oxford' UKSubmicron optical detection of neurotransmitter release

Tuesday !*:(%A L Amaral' M Alves' M Mota and E C FerreiraDepartamento de Tecnologia Química e Biológica' Instituto Politécnico de Bragança' PortugalApplication of image analysis techniques in dispersed and aggregated bacteria determination in wastewater treatment processes

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Wednesday ":%% Invited TalkK WandeltInstitute for Physical and Theoretical Chemistry' University of Bonn' GermanyUnderstanding solid/liquid interfaces using Fourier#filtering

Wednesday !%:%%M Santacroce' F Orsini' C Perego' C Lenardi' M Castagna' S A Mari' V F Sacchi and G PolettiIstituto di Fisiologia Generale e Chimica Biologica' University of Milan' ItalyVisualization of protein complexes on native plasma membrane of Xenopus laevis oocyte by atomic force microscopy

Wednesday !!:%%M J Moene' E H van Tol#Homan' P V Ruijgrok' T H Oosterkamp' J W M Frenken and M J RostKamerlingh Onnes Laboratory' Leiden University' The NetherlandsImage processing for video#rate scanning probe microscopy

Wednesday !!:(%J Ledieu and R N McGrathLSG$M CNRS' Nancy' France and Surface Science Research Centre' University of LiverpoolThe structure of quasicrystal surfaces analysed by scanning tunnelling microscopy

Wednesday !$:%%Q ChenLondon Centre for Nanotechnology' University College London' UKImaging the substrate through transparent organic adsorbate

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Invited Talk Monday !,:%%

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S Scheuring

Institut Curie' UMR#CNRS !&+' !! rue Pierre et Marie Curie' *)$(! Paris' France

The atomic force microscope (AFM) has become a powerful tool in structural biology allowing the investigation of biological samples under native#like conditions: experiments are performed in physiological buffer at room temperature and under normal pressure- Topographies of membrane proteins can be acquired at a lateral resolution of . !% Å and a vertical resolution of . ! Å- Using the AFM as an imaging tool' information concerning structure' function related conformational changes' and supramolecular assemblies' crucial for a complete understanding of membrane proteins' can be contributed- Furthermore' the AFM features such a high signal#to#noise ratio that membrane proteins can directly be visualized in native membranes- Thus' the native supramolecular assembly of the photosynthetic apparatus and its adaptation to different light intensities in native chromatophores of purple bacteria was studied [!]- The use and needs of image analysis of AFM data in membrane research will be discussed-

[!] Simon Scheuring and James Sturgis' Chromatic adaptation of photosynthetic membranes' Science ((((%%%%"""" ($%%)) ,+,�,+*

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R I Han' A Black*' AT French and B M Corcoran

Division of Veterinary Clinical Sciences' Royal (Dick) School of Veterinary Studies' The University of Edinburgh' Roslin' Mid#Lothian' UK*Department of Anatomy' National University of Ireland' Galway City' Republic of Ireland

Myxomatous mitral valve degeneration (MMVD) is the single most common acquired cardiac disease of the dog' and analogous conditions occur in other species' including humans- Recent data from our laboratory would suggest there are changes in the valvular interstitial cell phenotype in affected dogs- This is also reported for human mitral valve disease' but additionally an increase in cell numbers is also reported- The aim of this study' therefore' was to see if there is a similar increase in cell numbers in canine diseased valves and if there is a relationship between the numbers of interstitial cells in myxomatous areas of diseased valves and the overall severity of disease- Valves were collected at post mortem from normal and affected dogs and routinely processed for light microscopy- The degree of valve abnormality was graded from mild Grade I to severe Grade IV (Witney' J- Small Anim- Pract- !"*,)-

Morphological analysis of sections was carried out on a Macintosh PowerBook G, (Apple Computer' USA) using the public domain ImageJ software (National Institutes of Health' USA)- Areas of disease for each grade of severity (Grade I' n/&; Grade II' n/*; Grade III' n/+; Grade IV' n/()' and anatomically similar areas in normals (n/))' were selected in the distal zone of the valve leaflets (septal and mural)- The areas of myxomatous change were measured using the outline function- Cells were selected using the binary density threshold function and subjected to watershed segmentation- The total number of cells and the circularity of cells were measured and recorded in Excel data sheets for statistical analysis (ANOVA)-

Cell counts were compared between the four different grades and the normal controls' as well as between the septal and mural leaflets- The total mean cell density scores (cells per mm$) were; Grade I (septal/+),; mural/+%(); Grade II (septal/*%,; mural/**&); Grade III (septal/*$!; mural/)&*)' and Grade IV (septal/*$%; mural/)",)- No statistically significant differences were found between the total cell numbers per unit area of diseased tissue for each grade of disease- However' when these figures were compared with healthy normal valves (septal/!)%,; mural/!),$)' there was a significant difference (p0%-%%%!)- The circularity of cells in the dog valves were; Grade I (septal/%-)(; mural/%-)!); Grade II (septal/ %-)!; mural/%-,(); Grade III (septal/%-)%; mural/%-)$); Grade IV (septal/%-)%; mural/%-),) and the normal (septal/%-),; mural/%-),)- No significant differences found-


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The results of this study demonstrate there is a reduction in interstitial cell numbers in canine MMVD' and this contrasts with that reported for humans- This reduction in cell density occurs during the early stages of the disease' with a further gradual reduction as the disease progresses' but quickly reaches a threshold value- Throughout' there is a uniform interstitial cell density irrespective of the severity of the disease and the similarities in circularity suggest there is little change in cell shape in the disease process-


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C P Martin' P Siepman' M O Blunt' E Vaujour' N Krasnogor and P J Moriarty

School of Physics and Astronomy' University of Nottingham' UK

Although the self#assembly of nanoparticle (mono)layers and solids from solution continues to be an intensely active sub#field of nanometre scale science' there has been relatively little work performed to date on assembly/organisation far from equilibrium- The diverse range of structures that are produced under these conditions can be challenging to understand and classify- Among other techniques' Voronoi tessellation analysis and Minkowski morphometry can be employed to define these patterns quantitatively- Comparing the experimental Atomic Force Microscopy (AFM) images with those obtained by simulation can aid our understanding of the formation processes involved- Moreover' the use of these measures in conjunction with a 'genetic algorithm' enables the automated tuning of simulation parameters to reproduce morphologies seen in experiments-


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D Zhu' F Prin' A Gould and S N Pagakis

Confocal Imaging Analysis Lab' National Institute for Medical Research' London' UK

The sorting out of different populations of cells into distinct organs is central to the process of embryonic development- The mechanism underlying this segregation process appears to involve differential adhesion- However' relatively few useful methods for quantifying the degree of cell sorting between two cell populations and thus for measuring differences in cell affinities have yet been developed- Here we describe a generally applicable method' based on morphological image analysis' that quantifies cell sorting between two cell populations labelled with different fluorophores- After noise removal' a Canny filter is used to pick out double#labelled particles and then hole#filling using a morphological filter and region flagging algorithms are implemented to analyze and process the images- For each image' a cell#sorting ratio is calculated by dividing the sum of the lengths of particle boundaries shared between both cell populations by the total length of all the particle boundaries- We show how this method can be used to measure the extent of sorting out between two cell populations labelled with different fluorophores-


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J Walton and N Fairley

Corrosion and Protection Centre' School of Materials' University of Manchester' UK

Spectrum image datasets' that is a dataset containing a spectrum at each pixel in an image' may be obtained by the acquisition of images incremented in energy' known as parallel acquisition' or by scanning a probe and acquiring a spectrum at each point sequentially-

The ability to view such datasets as images or spectra is advantageous in that the images may reveal the presence of localised information' and the spectra allow the use of standard data processing techniques-

Such datasets may comprise as many as !%%% images of $)& x $)& pixels' and the time for acquisition would be prohibitive without the use of noise reduction procedures- Principal component analysis is ideally suited for this purpose' but is computationally intensive for such large datasets' since it scales as order n(' where n is the size of the covariance matrix- However by prior sorting the data by variance' principal component analysis may be applied to a much reduced dataset without incurring excessive computational times' allowing both the images and spectra to be processed-

Furthermore' classification of the pixels in the image abstract factors according to intensity' and summing their associated spectra' allows physically recognisable spectra to be localised within the image' without recourse to multivariate curve resolution-

The procedure is demonstrated by application to X#ray photoelectron spectrum image datasets for quantifiable surface chemical state microscopy' with all processing performed on a personal computer- The procedure is applicable to any spectrum image dataset' eg those obtained by EELS' or EDX' and to time lapsed datasets-


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Invited Talk Monday !":%%

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A M Newsam

Astrophysics Research Institute' Liverpool John Moores University' UK

In the last couple of decades' studies of gravitational microlensing have become an important tool in developing our understanding of the Milky Way galaxy- With recent improvements in telescope technology and image processing techniques' it is now possible to extend these studies to other galaxies � in particular our neighbour Andromeda- In this talk I will describe a particularly ambitious project' Angstrom' where we use Difference Image Analysis to search for tiny variations right in the core of Andromeda' allowing us to not only study the details of the galaxy' but opening up the possibility of finding the first extra�galactic planets!


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Invited Talk Tuesday ":%%

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A Thorsen

Institute of Marine Research' Bergen' Norway

Fecundity (number of eggs produced) is an important factor in fish reproductive biology- Not only does it give key information on the reproductive strategy of fish species' but also it is important in practical assessment of some fish stocks- The spawning stock biomass of the commercially important mackerel (Scomber scombrus) is estimated from the number of pelagic eggs found in the sea during triannual egg surveys and the mean number of eggs a female will produce each year- Therefore it is necessary to know the mean fecundity of the mackerel' which may vary from year to year-

Traditionally' fecundity of fish has been estimated using a time consuming gravimetric counting procedure- To do this the eggs in a small accurately weighed sub sample of the ovary is manually counted under the microscope and then raised to the total ovary weight- As an alternative' we developed the auto#diametric fecundity method for cod' which is far more time efficient- This method is based on computerized particle analysis of microscope images and a packing density (mean number of eggs per unit volume) formulae- The method has now been adopted and adapted by a number of laboratories in other countries and seems to work for several fish species- This presentation will deal with the principles and image analysis aspects of this method' which may be useful for other disciplines- Methods for diameter measurements of transparent pelagic fish eggs and grid counting on histological slides will also be presented-

Our image analysis lab at IMR is based on Macintosh computers using the freeware image analysis programs Image SXM' Object Image' and ImageJ- These programs have limited possibilities for direct internal image acquisition due to lack of camera drivers- Rapid image transference to these programs from specialised image acquisition programs will be demonstrated-


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M Safrai' D Darvish' Z Malik and A Weiss

Department of Biology' Bar Ilan University' Ramat Gan )$"%%' Israel

Malignant melanoma is the most life#threatening skin cancer- The disease manifests itself as a malignant transformation of normal melanocytes' so that they become nondifferentiated and rapidly dividing- A promising approach to the treatment of cancer involves the induction of the terminal differentiation and growth arrest of malignant cells- Melanoma is well known as a chemotherapy#resistant cancer' and it has been suggested that melanoma might be a suitable target for therapy with differentiation#inducing agents- Therefore' measurement of the state of differentiation of these cells is important-

Changes in dendritic phenotype' cell size' and nuclear size and shape' as well as other morphological parameters' are associated with the state of differentiation of cells- Cell morphology is also an important diagnostic tool' used by pathologists for assess the state of the malignancy and the patient's prognosis- The pathologist often must base his assessment on his qualitative impression of the tissue section- It would be helpful to be able to quantify morphological changes which are visually evident' so that objective parameters which express the level of differentiation can be measured-

In this talk' we will discuss morphological algorithms which we developed in order to follow the transition between the differentiated and nondifferentiated states- This transition was induced by treating B!& murine melanoma cells with butyrate' and following their subsequent growth in a microscope mounted incubator for *$ hours- Phase images of the cells were acquired every !) minutes- In some of the experiments' cells expressed a histone H$A#mRFP fusion' so that the nuclear morphology could be observed using fluorescence microscopy-

The morphological parameters which were chosen are based on concavity or circularity measurements- Concavity is defined as actual cell area/area enclosed by the cell�s convex hull- Circularity is calculated as ,π (area/perimeter$)- A perfect circle has a circularity of !-%' while a value that approaches %-% indicates an increasingly elongated polygon- Long dendritic processes were detected by comparing the convex hull area of an eroded cell image to the convex hull area of the original image- These measurements were chosen because they are based on observed changes in morphology' and because they are normalized- That is' they do not depend on absolute dimensions- All of these measurements are sensitive to dendritic phenotype' which is a clearly visible manifestation of differentiation-


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Besides the �static� morphological measurements just described' we consider also �dynamic� morphology- Here' we acquire images every )�!) seconds for five minutes' at various time points- Then' we look not only at the morphological parameters' but we also measure rates of change and variance of these parameters- Because the cells are very active' their morphology undergoes rapid changes about some mean- We are investigating whether the variance of the morphology may be a better measure of cell health than the static morphology- In this talk' we will present static and dynamic morphological measurements of both untreated and butyrate treated B!& murine melanoma cells-


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Tuesday !!:%%

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R Wightman' R Marshall and S Turner

Faculty of Life Sciences' University of Manchester' UK

Cellulose is the most abundant polymer on earth- It is synthesised by a large complex � the Cellulose Synthase Complex (CSC)- It is believed the CSC moves through the cell membrane synthesising a long cellulose fibre which is deposited at the cell wall- The long' cylindrical vessels that carry water through the plant are reinforced by rings of a secondary cell wall consisting mostly of cellulose- Beneath the secondary walls are large numbers of CSCs- Using confocal microscopy we have tried to visualise' in these vessels' movement of the CSC fused to a fluorescent reporter as it deposits cellulose to the secondary wall- Using a fixed narrow confocal bleach line coupled with measurements taken with Image SXM we have adapted a Fluorescence Loss In Photobleaching (FLIP) technique to show movement of the CSC around the vessel-

New CSCs are deposited at the cell surface by as yet an unidentified organelle- Using a combination of rapid time#lapse with an EMCCD camera coupled with standard deviation time#projections' we can see organelles containing labelled#CSCs travel along a one#way motorway system around the cell- Particle identification of time series has identified �fusion� events where organelles momentarily pause and deposit material at the cell surface-


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Tuesday !$:%%

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R H Fleming and D H Murray*

Roslin Institute' Edinburgh' UK and *University of Edinburgh' UK

Bone studies in domesticated birds are largely welfare#driven- Outlined below are $ main current research concerns; (!) osteoporosis in egg#laying hens' and ($) bone growth in rapidly growing broiler chickens-

(!) Medullary Bone (MB) is a woven bone type deposited during egg#laying in hens to provide a labile source of calcium for eggshell formation- Hens in#lay �borrow� their structural bone reserves to provide calcium for MB formation' whilst normal structural bone formation ceases- The net result is osteoporosis and bone fracture as MB is largely non#structural- Image analysis of hen bone is often complicated by the presence of MB but we have been able to separate bone types by differential staining of bone sections with toluidine blue (as MB is rich in the proteoglycan keratan sulphate) and subsequent area fraction measurements using NIH#Image !-&!- Cortical porosities in bone sections were determined with ImageJ v!-($ by fluorescing the eosin in H&E sections to remove soft tissue components- Numbers of active bone#resorbing cells (osteoclasts) were determined by tartrate�resistant acid phosphatase (TRAP) histochemistry and analysis with ImageJ- Bone formation rates were measured using bone�seeking fluorochromes and analysis with NIH#Image- Utilising these techniques (alongside measurements of radio#density and biomechanics) we have observed improvements in hen bone status by various interventions; nutritional ($$2 improvement via a combination of nutritional additives' P0%-%%!)' environmental ($%#$,2 improvement in bone characteristics in hens housed in an aviary compared to battery#caged siblings' P0%-%%!) and genetic ($(2 improvement in bone strength after & generations of selection for bone traits' P0%-%%!)-

($) Broiler chickens grow from ,%g to (kg in & weeks- To support this rapidly increasing body mass' leg bones grow circumferentially at around )%µm/d (compared to !%µm/d in laying strains)- As the population of bone#forming cells (osteoblasts) migrate outwards to support this rapid growth' there is a marked lack of infilling of cortical bone' leading to an extremely porous bone structure- We have utilised the techniques used in (!) to study bone status in fast (F) and slow (S) growing lines of broilers- Fluorochrome studies were also used to determine osteonal apposition rates (OAR) using Image Tool v$-%!- Results revealed that fast growing broilers had larger but more porous bones- There was a lack of cortical infilling in fast growing birds as indicated by OAR (F / !!-) µm/d' S / $+-$ µm/d)-


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Densities of mature bone cells were measured with Image Tool at the edge and within the bone- At the periosteal edge' osteocyte density was significantly higher in F than S strain birds at !, and ,$ days (P0%-%! for both)- Differences were not observed deeper within the primary osteons- These results suggest different rates of osteoblast differentiation and/or apoptosis between F and S birds and merit further study-

The image analysis techniques used throughout these studies are applicable to bone studies in general-


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Invited Talk Tuesday !,:%%

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R Heilbronner

Department of Geosciences' University of Basel' Switzerland

Crystallographic preferred orientations (CPOs) have a profound influence on the mechanical behaviour of crystalline solids- The bulk response of rocks to deformation or seismic waves' for example' depends (!) on the (tensor) properties of the constituent minerals' ($) on the lattice orientation of the grains with respect to one another and with respect to the applied stress or displacement boundary conditions' and (() on the geometry (size' shape) and spatial distribution of the individual phases-

A number of different techniques (Universal Stage' X#ray texture goniometry' electron back scatter diffraction (EBSD)' etc) are used to derive the pole density distributions (PDFs) and the orientation or misorientation distribution functions (ODFs)- From PDFs and ODFs the type and strength of the bulk CPO is assessed and the associated bulk properties (e-g-' seismic velocity) may be calculated- From PDFs of lattice directions that contain Burgers vectors' slip systems and deformation mechanisms are inferred-

In this contribution' however' we are not concerned with the orientation space- Instead' the focus is on mapping crystallographic orientations of rock forming minerals in real space' i-e-' in the plane of geological thin sections- We present and discuss orientation images (and derived images) obtained with the CIP method (computer#integrated polarization microscopy' http://www-unibas-ch/earth/micro/)- A number of applications to naturally and experimentally deformed rocks will be shown-

C#axis orientation images (COIs): The COI is composed of two image planes representing the azimuth and inclination of the c#axes with respect to the image plane- Using different colour look#up tables (CLUTs)' the c#axis orientations can be colour coded and their localization in the image can be visualized- Grains and orientation domains can be identified and the spatial correlation of grains and orientation domains can be investigated- Full orientation images consist of three image planes corresponding to three Euler angles (φ!' φ' φ$)- This imagery can only be obtained through EBSD-

Misorientation images: Calculating the angles of misorientation with respect to external or internal reference directions yields misorientation images- Misorientations along profiles yield interesting information concerning lattice deformation-


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Orientation gradient image: Calculating the angular difference between neighbouring pixels yields orientation gradient images- High gradients define grain boundaries- From misorientation gradient and orientation gradient images' grain boundary maps may be derived and grain size distributions may be determined-

Pole figures: From the $#d histogram of the azimuth and inclination planes' PDFs can be calculated and presented as c#axis pole figures- Masks can be used to derive partial pole figures for different parts of the microstructures-

Black Hills Quartzite' sheared experimentally in dislocation creep (lower right: Brazil quartz forcing block); sense of shear indicated- From left to right: ! # circular polarization' $ # COI (CLUT below)' ( # COI (CLUT below)' , # orientation gradient image' ) # three misorientation gradient images with respect to E' Up and N' superposed (CLUT below)- Center' between $ and (: c#axis polefigure of BHQ (without forcing block)- Width of image .+%%µm-


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Tuesday !):%%

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C D Barrie' A P Boyle and D J Prior

Department of Earth and Ocean Sciences' University of Liverpool' UK

The identification of plastic deformation within experimentally deformed pyrite (FeS$) grains is essential to understand what deformation mechanisms have occurred under what conditions- Previous studies have relied on techniques such as reflected light microscopy and backscatter electron (BSE) imaging with interpretations made on the basis of shape and optical homogeneity of grains which is very subjective- Recent studies (Boyle et al' !""+; Freitag et al' $%%,) have utilized forescatter orientation contrast (OC) imaging coupled with electron backscatter diffraction (EBSD) to determine dominant deformation mechanisms in pyrite grains- OC images are grey#scale images in which contrast reflects changes in crystal lattice orientation allowing plastic deformation to be readily identified' which is not possible using other techniques- These images are qualitative and so in order to generate quantitative results corresponding EBSD maps must be constructed- Each pixel in an EBSD map contains information on a single point and processing provides details such as; quantitative lattice rotation within individual grains and sub#grain boundary development- The data generated can be directly related to other images of the same area obtained using different techniques-

This study uses these techniques to compare four experimentally deformed samples under constant confining pressure of (%% MPa and a strain rate of $ x !%#, s#! at temperatures between ))%ûC and *%%ûC with the original undeformed material- OC imaging was used to observe how widespread' grey#scale variation was within grains and identify potential areas of study which could then be mapped using EBSD- The results show that variation in grey#scale in OC images varies as you deform the samples' with the levels of variation changing as temperature has increased- The OC image of the undeformed sample revealed homogeneous suggesting no lattice rotation was occurring- Images of the lowest temperature samples ())%/&%%ûC) contained significant variation in grey#scale within pyrite grains indicating abundant lattice rotation- Further analysis with EBSD identified a high density of low angle sub#grain boundaries within these grains (figure)- With increasing temperature the OC images showed a sharp decline in grey#scale variation within pyrite grains' and by *%%ûC pyrite grains appeared virtually homogeneous-


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The use of image analysis for both initial reconnaissance and further in#depth study is an essential technique in the analysis of pyrite- The results of this study show that forescatter OC images are a powerful tool in both identification and interpretation of the micro#structures in deformed pyrite grains- Future studies should consist of a combination of both reflected light and SEM based image analysis in order to fully understand the deformation mechanisms which have been operating-

))%ûC Sample: A- Reflected light image showing main phases present in sample (pyrite (py) and tennantite (tn))- B- Processed EBSD map showing pyrite grain and sub#grain boundaries- C- OC Image of the same area' arrows pick out variation in crystallographic orientation (grey#scale) within pyrite grains-

[!] Boyle A P' Prior D J' Banham M H and Timms N E' Mineralium Deposita ((((,,,, (!""+) *!�+![$] Freitag K' Boyle A P' Nelson E' Hitzman M' Churchill J and Lopez#Pedrosa M' Mineralium

Deposita (((("""" ($%%,) !%(�!!(


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Tuesday !&:%%

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N G D Kouankap' S Ganno and P T Azinwi

Department of Earth Sciences' University of Yaoundé !' P-O- Box +!$ Yaoundé' Cameroon

Microscopic study is an indispensable step in the determination of the petrographic characteristics of rocks- In Cameroon just like in most developing countries' simple polarizing microscopes of the $%th Century constitute the only available material for microscopic studies- A major difficulty encountered in the use of these instruments resides in the realisation of photomicrographs of the different parts of the thin section that require illustrations- The technique that has been used till present day has been inefficient and unsatisfactory- The setup that has existed till present day consists of an �Euromex� microscope with eyepiece fixation plates removable (removable eyepiece plate)- The principle consists of removing the eyepiece plate and then fixing a second one which is specially conceived' for it bears a metallic tube on which can easily be connected an argentic or analogical camera (that is using films)- This setup produce few images were then scanned so as to editable' finally mediocre to poor quality photomicrographs are obtained- Faced with this recurrent situation' we thought of setting up a new' semi modern' practical and very economical technique for photomicrographs combining digital camera and this simple polarizing microscope-

The new setup is based on the simple transmitted microscope' a digital camera and an adapter- The adapter is a hollow cylinder or a plastic cylinder whose diameter is greater than that of the objective of the digital camera- The adapter plays the role of extension of the eyepiece thereby facilitating movements (translational movements) of the zoom (objective) of the camera- This new technique has the advantage to clearly illustrate the microscopic descriptions; the observation is therefore of good quality' and is carried out in an easy manner- Group work is even easier- The new technique' which enabled to obtain in $%%) in the University of Yaoundé I the first numerical microphotographs' significantly contributed and facilitated the petrographic and structural study of geological formations-

The thin slide numerisation (without a scanner) enables the processing of the images with help of computer software such as Mesurin' Photoshop' or Corel Draw' to work on those pictures to meet up with expectations and interrogation raised at a big scale-


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Amongst the work includes:� The modification of the image that consists in the redrawing or integration of text

on the image with the possibility of defining the transparency' changing its dimensions' reframing and the modification of the format of the file;

� The extraction of a drawing according to an image; it enables' in an automatic or customised manner' to extract mineral contours' thus defining the relation existing among them;

� Point counting of an image' to enable the determination of the percentage of each mineral in thin slides-


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Invited Talk Tuesday !&:(%

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K L Brain

Department of Pharmacology' University of Oxford' UK

The brain communicates with the body through hard#wiring provided by peripheral nerves- Electrical signals' originating in the brain' actively propagate along these nerves to their ends' the nerve terminals- The electrical signal causes the release of chemical substances (neurotransmitters) from nerve terminals onto target organs such as muscle- The most sensitive methods for detecting neurotransmitter release have' for half a century' been electrical- More recently' optical approaches having allowed unprecedented spatial resolution of neurotransmitter release while achieving good temporal resolution and sensitivity- Here' one such method is described and the problems associated with image acquisition' processing and analysis are considered-

The model system consists of the nerves and smooth muscle of the mouse vas deferens (part of the male reproductive tract)- In this system' the neurotransmitter ATP is intermittently released from nerves and acts on smooth muscle cells to cause contraction- In doing so' the ATP causes a local change in Ca$3 concentration in the adjacent smooth muscle [!]- Using fluorescent Ca$3 indicators (such as Oregon Green ,++ BAPTA#!) to fill the smooth muscle' this local Ca$3 transient can be detected and the site and relative amount of neurotransmitter release inferred- In essence' the challenge is to be able to detect and measure rare focal changes in the fluorescent signal occurring at unspecified locations over image fields of about !%%x!%% µm in an organ that moves (as the smooth muscle contracts)' using automation so that thousands of images can be efficiently analysed-

Movement is reduced mechanically' by pinning the organ on a Sylgard#covered microscope slide on an upright Leica SP$ confocal microscope' and pharmacologically- To increase the signal/noise ratio a wide confocal pinhole is used with acquisition rates of , frames/s- The nerves are simulated electrically' to induce single action potentials; stimuli and imaging are synchronised with a TTL pulse from the microscope- Off#line' image analysis is performed with NIH Image' Image SXM or Image J- Movement of the tissue is corrected by using the �Auto Register� function in Image SXM' or by automated tracking of a bright marker between image frames- Focal changes in the fluorescent signal are detected by calculating the normalised ratio of each image frame with the immediately preceding frame- Using the �Particle Analysis� procedure of NIH Image (and its spin#offs) on the ratioed image sets allows the automated detection of local Ca$3 transients-


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Approaches to account for areas of low signal intensity (and hence a ratio with a large error)' background signal' and semi#automated processing of derived data are consider- This style of optical approach is of emerging interest within both the peripheral [$] and central nervous systems [(]' encouraging the efficient optimisation of experimental design and image analysis-

[!] Brain K L' Jackson V M' Trout S J and Cunnane T C ($%%$) J- Physiol- )))),,,,!!!!' +,"#+&$[$] Heppner T J' Bonev A D and Nelson M T ($%%)) J- Physiol- ))))&&&&,,,,' $%!#$!$[(] Emptage N' Bliss T V P and Fine A (!""") Neuron $$$$$$$$' !!)#!$,


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Tuesday !*:(%

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A L Amaral' M Alves' M Mota and E C Ferreira

Departamento de Tecnologia Química e Biológica' Instituto Politécnico de Bragança' Campus de Santa Apolónia' )(%!#+)* Bragança' Portugal

Image processing and analysis methodologies are considered nowadays as extremely useful tools in a wide range of applications- One of their main advantages resides on the ability to remove human subjectiveness and extract quantitative data that would be either very difficult or indeed impossible to obtain otherwise as well as to avoid extremely tedious or time#consuming tasks for the researcher- Therefore' in the last years it has been reported an exponential increase on the use of image processing and analysis techniques in the WWTP aerobic and anaerobic processes-

Ideally an aerobic microbial aggregate should be composed by a balanced number of filamentous and floc#forming (zoogleal) bacteria' have an adequate dimension' high robustness and settling ability to obtain a final clarified effluent and low organic matter contents- Classical methods for filamentous and zoogleal bacteria assessment have relied on manual microscopic counting- However' these techniques are quite straining' imprecise and time#consuming' which halted their implementation in a daily basis in the WWTP laboratories- Bearing this in mind' an image processing and analysis methodology was proposed and subsequently tested in the monitoring of bulking phenomena in a municipal WWTP-

Regarding the anaerobic processes' the granular structure of the microbial aggregates within the digester is of crucial importance- In adverse conditions the granular biomass may deteriorate affecting the reactor stability leading to biomass wash#out phenomena and' hence' to a decrease on the reactor efficiency- Although it is common knowledge that the granulation process is coupled with macroscopic morphological changes' systematic observations have not yet been used widespread due to the fact that such methodology revealed to be quite tedious and difficult to implement- Therefore' the use of image analysis techniques with the macro and microscopic observations may reveal as a quite useful tool as it allows for a methodical study of both the free filamentous and the aggregated biomass-


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In the scope of this work image processing and analysis methodologies were applied in order to obtain the morphological data subsequently treated by multivariable statistical techniques such as partial least squares- Globally this study comported two main axes: monitoring of a WWTP with respect to the aerobic activated sludge process and of an EGSB digester regarding the anaerobic granulation process-

Regarding the WWTP aerobic process the high SVI values confirmed the existence of a severe bulking problem that was proven to be of filamentous nature by the results from the image analysis methodology- Moreover the dispersed bacteria per suspended solids ratio was shown to be related with the SVI values for WWTP with filamentous bulking phenomena and a second relationship was also established between the TSS and the total aggregates area- With respect to the anaerobic granulation process the results showed an increase on the aggregates size and contents within the reactor throughout the experience- Furthermore' it was found possible to determine the granulation time by the analysis of the aggregates morphology as well as the mechanism of granulation-


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Invited Talk Wednesday ":%%

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K Wandelt

Institute for Physical and Theoretical Chemistry' University of Bonn' Germany

Electrochemical surface science increasingly gains importance as the basis of our understanding of technologically relevant processes at solid/liquid interfaces' such as thin film growth' deposition or etching of nano#structures' electrocatalysis etc- In#situ electrochemical scanning tunneling microscopy (ECSTM) is a powerful tool to investigate structures and phase transitions at metal/electrolyte interfaces- Beyond the mere imaging of structural motifs Fourier filtering of ECSTM images provides extra insight into the epitaxial relationship and the absolute adsorption sites of an adsorbed layer with respect to the substrate surface- This will be demonstrated with several examples on a Cu(!!!) electrode' including the adsorption of chloride and sulphate anions [!' $]' the growth of a cadmium chloride film [(]' and structural phase transitions within a sulphide overlayer as a function of electrode potential [,]-

[!] Ch- Stuhlmann' B- Wohlmann' Z- Park' M- Kruft' P- Broekmann' K- Wandelt' in: Solid#Liquid Interfaces (Eds- K- Wandelt' S- Thurgate)' Topics Appl- Phys- ++++))))' !""#$$! ($%%()

[$] P- Broekmann' M- Wilms' M- Arenz' A- Spänig' K- Wandelt' in: Solid#Liquid Interfaces (Eds- K- Wandelt' S- Thurgate)' Topics Appl- Phys- ++++))))' !,!#!"* ($%%()

[(] J- Hommrich' S-Hümann' K- Wandelt' Faraday Discuss- !!!!$$$$!!!!' !$,#!(+ ($%%$)[,] A- Spänig' PhD#Thesis' University Bonn ($%%,)


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Wednesday !%:%%

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M Santacroce' F Orsini' C Perego' C Lenardi' M Castagna' S A Mari' V F Sacchi and G Poletti

Istituto di Fisiologia Generale e Chimica Biologica �Giovanni Esposito�' University of Milano' Italy

Atomic force microscopy (AFM) was used to characterize the plasma membrane of Xenopus laevis oocytes- Images were obtained in air in contact mode collecting the topography and deflection mode signals simultaneously- Deflection mode images' although do not give quantitative information of the visualized structure heights' result very useful in giving a direct imaging of the small corrugations on the sample surface' and in analyzing the density and lateral dimension of the visualized structures-

Regions with comparably sized and densely packed structures arranged in an orderly manner were visualized and dimensionally characterized- The lateral dimension of structures visualized on the external side had a normal distribution centred on $)-) 4 %-( nm (mean value 4 S-E-)' whereas that on the intracellular side showed a normal distribution centred on (%-$ 4 %-+ nm- The height of the protrusions was $#) nm on the external side' and !#( nm on the intracellular side- The mean number of structures on the external and intracellular sides of the plasma membrane was about !%%%/mm$ and +)%/mm$ respectively- Trypsin treatment greatly decreased the size of the membrane protrusions' thus confirming the proteic nature of the structures-

Moreover' two different and easily identifiable arrangements' hexagonal and square packing' were recognized in ordered regions and analyzed through Fast Fourier Transform (FFT) analysis which provides a convenient representation of the spatial periodicity and amplitude of the roughness and is very effective when ordered surface features are observed- For the first arrangement' the FFT analysis shows that the more intense spatial frequency is at $* nm' whereas for the second one at $( nm- The hexagonal packing allowed to identify a hexagonal unit cell with a measured internal angle of about !!+° while the square packing allowed to identify a square unit cell with a measured angle of about "%°- The image showing these ordered arrangements was processed applying a FFT filter to remove the high frequency contribution and improve the image quality-

The hexagonal and square packings indicate that in the oocyte plasma membrane are present microdomains where the protein complexes arrange in order to maximize their number on the membrane-


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Our results confirm that plasma membrane is not an homogeneous structure but has domains that can be visualized' in this case as an ordered arrangement at submicrometer level' as described on the basis of a dynamically structured mosaic model [Vereb et al-' $%%(]-

Vereb G' Szöll si J' Matkò J' Nagy P' Farkas T' Vigh L' Màtius L' Waldmann TA' Damjanovich S- $%%(- Dynamic' yet structured: The cell membrane three decades after the Singer#Nicolson model- Proc- Natl Acad- Sci- USA !%%: +%)(#+%)+


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Wednesday !!:%%

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M J Moene' E H van Tol#Homan' P V Ruijgrok' T H Oosterkamp' J W M Frenken and M J Rost

Kamerlingh Onnes Laboratory' Leiden University' $(%% RA Leiden' The Netherlands

Since its invention' only $) years ago' scanning tunneling microscopy (STM) has developed into one of the most important techniques for real#space surface observation with atomic#scale resolution- Due to its revolutionizing applications in surface science' it also has developed into a widely used tool for nanotechnology- In addition' alternative sensing methods' such as used in the atomic force microscope (AFM)' have enabled applications in new challenging fields like catalysis' friction' and even biological samples-

Despite the clear strengths of scanning probe microscopes (SPMs)' there are still drawbacks on many aspects- The most notable drawbacks are the long image recording time [!] and the amount of experience that is required to operate such an instrument-

In an attempt to push the limits and to speed#up SPM measurements to video#rate' we are continuously developing SPM technology including the software' the electronics' and the mechanics- Recently we reached record#breaking frame rates up to $%% Hz' while still obtaining atomic#scale resolution [$]-

The increased frame#rate requires very fast image processing' both for the data display during the measurements and for the quantitative analysis afterwards- The following example demonstrates the software requirement: in only ten minutes' a measurement at maximum speed yields !$% GB of data-

In this presentation' we will discuss the difference in requirements between acquisition and analysis- Using examples of real measurements' we will point out the problems' demands' and first solutions regarding the software- Topics include image processing for tasks of stabilisation' background subtraction' and feature recognition- For these tasks we apply techniques' such as fast normalized cross#correlation' most common normal statistics' and Hough transformation-

[!] The image acquisition is inherently time�consuming' due to the scanning motion of the instrument-

[$] M J Rost' L Crama' P Schakel' E van Tol et al-' Rev- Sci- Instrum- ****&&&& ($%%)) %)(*!%


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J Ledieu and R N McGrath*

LSG$M CNRS' ),%,$ cedex Nancy' France*Department of Physics and Surface Science Research Centre' University of Liverpool' UK

Over the past forty years' the structures of crystal surfaces have been best#characterised using diffraction techniques- The diffraction data recorded are compared with calculated diffraction spot intensities based on trial periodic structures and using software requiring a unit cell- A similar approach to the study of quasicrystal surfaces is hampered by their lack of translational symmetry- Quasicrystals are non#periodic systems' well#ordered' exhibiting discrete diffraction patterns with ) or !%# fold rotational symmetries depending on the samples and on the surface orientation- Consequently' the aperiodic nature of quasicrystal limits the use of diffraction tools into elucidating their surface structure- Hence scanning tunneling microscopy (STM)' being an imaging technique' provides real space information which can be analysed and interpreted without the recourse to a periodic formalism-

Here we will show how Fourier filtering procedure' calculations of autocorrelation and radial distribution functions from STM images have been vital to determine the )#fold quasicrystal surface structure- With the increasing computational power available nowadays' it has been possible to simulate STM images using density functional theory calculations and to compare them with our experimental results-

Finally' adsorption studies have been carried out on the )#fold surface and by image processing it has been possible to identify the nucleation site of these added atoms/ molecules on this quasicrystalline surface-


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Wednesday !$:%%

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Q Chen

London Centre for Nanotechnology' University College London' UK

It is always important to investigate the adsorption sites with atomic resolution in STM- However' with adsorbate on the surface' it becomes difficult to identify the underneath substrate structure- Normally' an extended substrate structure from the nearby clean substrate is used as reference to the substrate under the adsorbate' which may or may not be correct-

In order to directly identify the structural relationship between the adsorbate and its underlying substrate' we have developed an imaging method by adjust the relative tunnelling conductance between different junctions- A tunnelling junction under the STM tip is constructed with tip#adsorbate and adsorbate#substrate junctions- The tunnelling topography is determined by one of those with least conductive junction- In this presentation' we demonstrate the STM study of tetracene on p($x!)#O on Cu(!!%) surface- By reducing the tip#molecule distance' we show that the molecule adsorbate gradually becomes transparent while the image topography becomes dominated by the substrate features- This variation of topography is quantitatively controllable and completely reversible- Therefore' the method allows us directly identify the adsorption sites for the adsorbate without disturb the adsorption structure- The mechanism for this controllable invisible adsorbate is also discussed-


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Adeleye' Patrick Hydraulic Equip Dev Inst nat_issues@email$me-net

Almond' Nick University of Liverpool n-almond@liv-ac-uk

Amaral' Luís Inst Politéc Bragança lpamaral@ipb-pt

Arinze' Ajemba Geological Survey Nigeria trade_rewards@yahoo-com

Barrett' Steve University of Liverpool s-d-barrett@liv-ac-uk

Barrie' Craig University of Liverpool c-d-barrie@liv-ac-uk

Bowfield' Andrew University of Liverpool a-bowfield@liv-ac-uk

Brain' Keith University of Oxford keith-brain@pharmacology-ox-ac-uk

Cardus' Rachel International Paint rachel-cardus@internationalpaint-com

Chapman' Jim Olympus mbaggs@olympus-uk-com

Chen' Qiao University College London qiao-chen@ucl-ac-uk

Chungong' F Louis Umeå University fortolouis@yahoo-com

Convery' Joanne University of Liverpool joanne-convery@liv-ac-uk

Efemini' Gabriel Hydraulic Equip Dev Inst nat_issues@email$me-net

Fleming' Bob Roslin Institute bob-fleming@bbsrc-ac-uk

Francis' James Media Cybernetics jfrancis@mediacy-com

Frank' Okeke Geological Survey Nigeria trade_rewards@yahoo-com

Gerber' Jamie University of Liverpool jngerber@liv-ac-uk

Gilbert' Stephen University of Leeds s-h-gilbert%,@leeds-ac-uk

Goncalves' Rui Pedro Institut Curie ruipedro-goncalves@curie-fr

Han' Richard University of Edinburgh r-i-han@sms-ed-ac-uk

Hathiwala' Raj Olympus raj@olympus-uk-com

Heilbronner' Renee University of Basel renee-heilbronner@unibas-ch

Holland' Chris University of Oxford cholland@jesus-ox-ac-uk

Isted' Greg University of Liverpool gregisted@hotmail-com

Kearns' Victoria University of Liverpool vkearns@liv-ac-uk

Kouankap' Djibril University of Yaoundé kouankap@yahoo-fr

Ledieu' Julian LSG$M CNRS ledieu@lsg$m-org

Leishangthem' Khaba Kharkov National Univ khaba(&@yahoo-com

Leung' Lydie University of Liverpool l-leung@liv-ac-uk

Lloyd' Roslyn LOT Oriel roslyn@lotoriel-co-uk

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LLLLiiiisssstttt ooooffff DDDDeeeelllleeeeggggaaaatttteeeessss

McGrath' Ronan University of Liverpool r-mcgrath@liv-ac-uk

Martin' Christopher University of Nottingham ppxcpm!@nottingham-ac-u

Martin' David University of Liverpool davidm@liv-ac-uk

Moene' Martin Leiden University m-j-moene@eld-physics-leidenuniv-nl

Moriarty' Philip University of Nottingham philip-moriarty@nottingham-ac-uk

Newsam' Andrew Liverpool John Moores amn@astro-livjm-ac-uk

Orsini' Francesco University of Milano francesco-orsini@unimi-it

Preston' Matt Media Cybernetics mpreston@mediacy-com

Safrai' Michal Bar#Ilan University michael_goldfish@yahoo-com

Santacroce' Massimo University of Milano massimo-santacroce@unimi-it

Saturday' Osawaru Geological Survey Nigeria trade_rewards@yahoo-com

Schofield' Amy University of Liverpool amy_lou@hotmail-com

Thompson' Gill University of Bradford j-b-thompson@bradford-ac-uk

Thorsen' Anders Institute Marine Research anders-thorsen@imr-no

Walton' John University of Manchester john-walton@manchester-ac-uk

Wandelt' Klaus University of Bonn k-wandelt@uni#bonn-de

Wearing' Lisa University of Liverpool l-h-wearing@liv-ac-uk

Weiss' Aryeh Bar#Ilan University aryeh@cc-huji-ac-il

Wightman' Raymond University of Manchester raymond-wightman@man-ac-uk

Young' Heath LOT Oriel heath@lotoriel-co-uk

Zhu' Daan Nat Inst Medical Research dzhu@nimr-mrc-ac-uk

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Steve Barrett s-d-barrett@liv-ac-uk

Ronan McGrath r-mcgrath@liv-ac-uk

David Martin davidm@liv-ac-uk

with thanks toMarj Robson m-robson@liv-ac-uk

Nicola Gilmore n-gilmore@liv-ac-uk

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Documents

IAfM-Booklet dr12.cwk - The University of Liverpool