MIASMA case study - Microcirculation Analysis - University of ...

PHYS871 Clinical Imaging Applica4ons / MIASMA 

PHYS871 Clinical Imaging Applica>ons 

Introduc>on 

Microscopy Image Analysis SoDware for Medical Applica4ons 

What is MIASMA? 

A brief descrip4on of some of the projects 

A more detailed look at one project 

Dr Steve Barre* 

April 2013 


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MIASMA 


So what can a physicist do to make an impact in medicine? 

Background in nanoscale physics 

Exper>se in image analysis of scanning 

microscopy images (STM, AFM, SEM) 

Recognising molecular shapes 

(adsorp>on geometry) 

Liverpool Medical Imaging Network (LMI-‐Net) workshops 

Put me in touch with medics who had image analysis problems 

Some researchers within UoL, some clinicians in hospitals 

Resulted in a number of collabora>ons 

Iden>fying molecular posi>ons 

(substrate registra>on) 

PHYS871 Clinical Imaging Applica4ons / MIASMA / Background 

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PHYS871 Clinical Imaging Applica4ons / MIASMA / Background 

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Dr Steve Barre? 

April 2013

What is MIASMA? 


Microscopy Image Analysis Software for Medical Applications 

MIASMA is the collective name for a number of projects involving image analysis in which I am collaborating with medics. Since about 1993 I have been 

writing software for image analysis of scanning microscopy images, principally for applications in nanoscience and related disciplines. The software that I 

have written, and continue to develop and expand, is Image SXM. Although written for scanning microscopy applications, I have found that Image SXM is 

an excellent platform on which to develop specialist image analysis solutions for the specific needs of users, including those who obtain images from light 

microscopes. MIASMA is the result of a number of these specialist applications having some common ground and so benefiting from being considered as 

part of a larger, overarching project. 

What are the MIASMA projects? 


Intracellular Air Pollution Particulates 

Collaborators 

Aims 

SPM Image Display 

Projects include… 

Carbon par>culate ma*er in lung cells (lung cancer) 

Parasite analysis (malaria) 

Blood flow veloci>es in capillary networks (meningi>s) 

Re>nal image analysis (diabetes) 

Parasite morphology and development (leishmania) 

Assessing an>bio>c treatments (tuberculosis) 

Malaria Parasites 

Microcirculation Flow 

Dr Stephen Gordon 

Liverpool School of Tropical Medicine 

Dr Duncan Fullerton 


Collaborator 

Professor Alister Craig 


i) To identify particulate matter and differentiate 

it from cell cytoplasm. 

ii) To measure the area of particulate matter 

relative to that of the cell cytoplasm. 

Documentation MIASMA-PMA-v7.pdf 

Aim 

To identify malaria parasites and differentiate 

them from background features. 

Documentation MIASMA-PCA-v5.pdf 

Collaborators 

Aims 

Dr Enitan Carrol 

Institute of Child Health, UoL 

i) To identify capillaries in videos of capillary 

networks and measure capillary vessel density. 

Dr Richard Sarginson 

Alder Hey Children's Hospital 

ii) To measure blood flow speed as a function of 

capillary diameter. 

Dr Fauzia Paize 

UoL and Liverpool Women's Hospital 

Documentation MIASMA-MCA-v5.pdf 

Retinal Imaging 

Collaborators 

Aims 

Professor Simon Harding 

Ophthalmology Research Unit, UoL 

Dr Yalin Zheng 

Ophthalmology Research Unit, UoL 

To identify specific features such as: 

Blood vessel network 

Optic disc 

Haemorrhages 

Exudates 

PHYS871 Clinical Imaging Applica4ons / MIASMA / Background 5 

PHYS871 Clinical Imaging Applica4ons / MIASMA Documentation Not yet available 

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http://www.liv.ac.uk/~sdb/MIASMA/ 

Page 1 of 3 

MIASMA 

14/05/12 12:20 

Parasite Morphology 

Collaborators 

Aims 

SPM Image Display 

Microcircula>on Analysis 

Lymphocyte Flow 

Dr Rod Dillon 


Mr Hector Diaz 


i) To identify leishmaniasis parasites. 

ii) To identify the developmental stage of the 

parasites by the shape and size of the parasite 

bodies and flagella. 

Documentation Not yet available 

Take one MIASMA project as an example… 

Blood flow veloci>es in capillary networks (meningi>s) 

Collaborator 

Aims 

Dr Carlo Laudanna 

Department of Pathology 

University of Verona 

i) To identify lymphocyte cells flowing through a 

glass capillary. 

ii) To measure the length of time that cells are 

arrested by or rolling along the capillary wall. 

Documentation MIASMA-LFA-v4.pdf 

Bacilli Lipid Bodies 

Collaborator 

Aim 

Dr Derek Sloan 

Clinical Sciences, UoL 

To measure the number of bacilli that contain 

lipid bodies. 

Documentation Not yet available 

Fibrillin Microfibrils 

Collaborator 

Aim 

Dr Riaz Akhtar 

Ocular Biomechanics Group 

School of Engineering, UoL 

To speed up the analysis of microfibrils by semiautomating 

the process of identifying microfibril 

beads and calculating their xy coordinates. 


Documentation MIASMA-MFA-v2.pdf 

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PHYS871 Clinical Imaging Applica4ons / MIASMA / Microcircula4on 

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Who is working on MIASMA projects? 

Apart from me, I recruite project students from Physics degree programmes and Summer students 

Name Status Project 

Martin Renvoize F303 MPhys Year 4 student Microcirculation Analysis 

Fergus Dunn F350 BSc Year 3 student Retinal Imaging (diabetic retinopathy) 


Simon Blaen F350 BSc Year 3 student Parasite Morphology 

Ben Wadsworth Nuffield Bursary student Malaria Parasites 

Hannah Burton Nuffield Bursary student Retinal Imaging (optic disc recognition) 

James Dorman Nuffield Bursary student Parasite Morphology 

April 2013 

Paul Mulligan F303 MPhys Year 4 student Parasite Morphology 

Kathryn Rose F300 BSc Year 3 student Lipid Body Analysis


Sepsis 

Magnifica>on 

Video Stability 

PHYS871 Clinical Imaging Applica4ons / MIASMA / Microcircula4on / Sepsis 9 

PHYS871 Clinical Imaging Applica4ons / MIASMA / Microcircula4on / Video Stability 

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Rota>on 

More likely, all of these… 

…plus ven>la>on, heartbeat 


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April 2013




What informa>on can be extracted? 

How should the microcircula>on be quan>fied? 

What (manual) scoring systems exist? 

Percentage of perfused vessels (PPV) 

( Perfused = flow exists for > 50% of the >me ) 

Microcircula>on Flow Index (MFI) 

( Is the flow ‘intermi*ent’ or ‘sluggish’ or OK? ) 

Calcula>on of blood flow speeds 

• Stabilisa>on of the video 

• Iden>fica>on of the blood vessels (which are invisible) 

• Isola>on of each capillary vessel 

• Analysis of the movement of the blood cells 

Quan>fica>on of the flow distribu>on (PPV and MFI) 

• Flow speed as a func>on of >me 

• Flow speed as a func>on of vessel diameter 

• Varia>ons in flow speeds across the vessel network 

PHYS871 Clinical Imaging Applica4ons / MIASMA / Microcircula4on / Scores 

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PHYS871 Clinical Imaging Applica4ons / MIASMA / Microcircula4on / Scores 

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Calcula>on of blood flow speeds 

• Stabilisa>on of the video 

fica>on of the blood vessels (which on of each capillary vessel cle Analysis 

• Analysis of the movement of the blood cells




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Terahertz Imaging 

Terahertz Imaging 

The latest MIASMA project… 

Imaging of biopsies with THz radia>on (cancer) 

Is there a pre-‐cancer signature in the infrared absorp>on? 

Is there a pre-‐cancer signature in the infrared absorp>on? 

ALICE is an accelerator at 

Daresbury Laboratory 

that is an intense source 

of infrared light with a 

Topography IR λ = 7.3 µm IR λ = 8.6 µm 

frequency of THz. 

This research shows poten>al but is s>ll at an early stage. 

PHYS871 Clinical Imaging Applica4ons / MIASMA / THz Imaging 

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PHYS871 Clinical Imaging Applica4ons / MIASMA / THz Imaging 

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April 2013

MIASMA case study - Microcirculation Analysis - University of ...

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