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[SA_Scat] PDRA and PhD posts

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  • Subject: [SA_Scat] PDRA and PhD posts
  • From: "Terrill, Nick \(DLSLtd,RAL,LSCI\) via sa_scat" <sa_scat@iucr.org>
  • Date: Wed, 13 Jan 2021 18:15:41 +0000
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Dear All,



As part of new project between QMUL, UCL, UoM, Diamond and ESRF, we have two PDRA and one PhD posts. EPSRC funded, the project will couple synchrotron micro-tomography and SAXS to enable imaging of fibrillar tissue in joints and intervertebral discs. The bioengineering challenge is to determine the correlated 3D deformation and structural changes at the molecular-, fibrillar-, and cell-matrix length-scales under physiological load in intact tissue, and how these alter in ageing, injury and disease. You will be based at Harwell Campus where Diamond Light Source is located. The details on the PDRF and PhD posts are below. Please forward on to anyone you think might be interested.



Research Fellow in Tomo-SAXS: Dynamic Tomographic and SAXS Imaging of Joint Mechanics, see http://bit.ly/TomoSAXS_RF01

Your goal will be to adapt existing in situ rigs for physiological loading for CT and SAXS imaging, developing experiments and analysis codes to measure strains at the nanoscale using digital volume correlation. A second PDRF will lead the 3D-SAXS development.



PhD studentship: Macro-to-molecular correlative X-ray imaging of strain during spinal joint loading, w. Peter D Lee, Federico Bosi and Himadri S Gupta (QMUL). See https://bit.ly/TomoSAXS_PhD1<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbit.ly%2FTomoSAXS_PhD1&data=04%7C01%7C%7C85929bd8a0f24e3583bc08d8a28ae902%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637438064776986425%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=v%2BNNlfHbd0DvYXXxbgGH8TxonD4J77X1F2PeEi1KEgc%3D&reserved=0>

You will use two imaging modalities, phase contrast tomography (pCT) and digital volume correlation (DVC), to measure strains at the nanoscale in whole joints using a unique in situ biomechanical loading device. You will analyse these results using pCT/DVC to predict the functional alterations in micromechanics in intact, injured joints, providing new insights into the function of the human body in health and disease. You will be working with two PDRAs who will be developing the techniques.



The PDRA post will be advertised soon and  will focus on developing 3D SAXS analysis for nanoscale mechanics in musculoskeletal tissues and organs, using diffraction models for collagen fibril scattering. They will correlate 3D SAXS with CT-imaging in physiological and injurious loading of such organs.



Note that we have two PDRA and two PhD studentships on an complementary project, which is part of  of an international, interdisciplinary Chan Zuckerberg Initiative funded joint UCL-ESRF-Hannover-Mainz project to develop a new tomography imaging modality (HiP-CT) using the world’s brightest synchrotron, ESRF-EBS, to scan whole human bodies with 1um local resolution (see  https://mecheng.ucl.ac.uk/hip-ct<https://mecheng.ucl.ac.uk/hip-ct/>). You will work with the bio-modelling, bio-Imaging, and AI groups at UCL, together with Medics in Germany, and X-ray physicists in France. The overall project goal is to develop novel techniques to help better understand human physiology and how diseases such as Covid-19 injure our organs and other soft and hard tissue.

The two PDRF posts on the CZI project are:

  1.  Research Fellow in X-ray Imaging: Whole Organ to Cellular Resolution (based at ESRF) Profs. Peter D Lee, Simon Walker-Samuel and Drs. Paul Tafforeau (ESRF) and Claire Walsh.  See: http://bit.ly/HiP-CT-PDRA01

Your role will be to help develop this tomography technique (HiP-CT<https://mecheng.ucl.ac.uk/hip-ct/>) focussing on developing and implementing machine learning correlative image analysis techniques, performing scans and interpreting the results, working with clinicians and biologists worldwide..

  1.  Research Fellow in Tomographic Image-based Dynamic Whole Organ Modelling (based at UCL or Harwell, but with long stays at ESRF)  Profs. Peter D Lee, Rebecca Shipley and Drs. Paul Tafforeau (ESRF) and Claire Walsh.  See: http://bit.ly/HiP-CT-PDRA02.

Your goal will be to perform computational simulations of dynamic biological processes including blood flow and joint biomechanics (validated via in situ digital volume correlation). You will also work with other researchers to help optimise the reconstruction and segmentation algorithms.



The two PhD posts on the CZI Project are:

  1.  Deep Learning guided Imaging to correlate imaging from a whole organ to cellular level, w. Prof. Simon Walker-Samuel and Drs Claire Walsh & Joseph Jacobs.  See: https://bit.ly/HiP-CT_PhD01<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbit.ly%2FHiP-CT_PhD01&data=04%7C01%7C%7C85929bd8a0f24e3583bc08d8a28ae902%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637438064776976431%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KBgvDMz8%2BNyh2yPLdB9gIsZS%2B1tosyOB7zkqKDct204%3D&reserved=0>

This project will initially develop and apply deep learning techniques to segment HiP-CT data (airways, blood vessels, cells, etc.) to enable biological insights to be drawn and for further biophysical simulations. A secondary aim will be to explore more advanced machine learning techniques such as generative adversarial networks, in order to correlate HiP-CT data with images from other modalities (such as histology, lightsheet, MRI and CT). This type of analysis will enable substantially better interpretation of HiP-CT so that it can provide quantitative biological and medical insights.



  1.  Imaging to inform models of whole organ behaviour in health and disease, w. Profs. R. Shipley & Peter Lee.  See: https://bit.ly/HiP-CT_PhD02<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbit.ly%2FHiP-CT_PhD02&data=04%7C01%7C%7C85929bd8a0f24e3583bc08d8a28ae902%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637438064776976431%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Olr6GrhupauXMtts%2F41mvgYCFJkFvcCtD8OAViZlw3Y%3D&reserved=0>

You will use segmented synchrotron data from a variety of organs as input for established and novel models of: blood flow prediction, air flow prediction, drug delivery. Using these models, you will predict functional information from segmented structural information, providing new insights into the function of the human body in health and disease (including Covid-19).





Prof. Peter D. Lee, FREng

RAEng Chair in Emerging Technology

Rm 5.14 Malet Place Eng. Building,  UCL Mechanical Engineering<https://mecheng.ucl.ac.uk/>, Torrington Place, London, WC1E 7JE

Harwell Campus Laboratory: Materials, Structures and Manufacturing Group  (MSM@H), Rm G17, Research Complex at Harwell, RAL, Didcot, OX11 0FA

Home page<https://mecheng.ucl.ac.uk/people/profile/peter-lee/> / Google Scholar<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.co.uk%2Fcitations%3Fuser%3DAY8iG6sAAAAJ%26hl%3Den&data=04%7C01%7C%7C85929bd8a0f24e3583bc08d8a28ae902%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637438064776996419%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=HHtQHF7OC2n0WWc6DvmVyG5619xYd7Zs8xcm9Gf98PM%3D&reserved=0>

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