A cross-resolution preclinical imaging framework based on MRI and light sheet microscopy to assess post-stroke axonal regrowth
Lead Research Organisation:
University of Nottingham
Department Name: School of Medicine
Abstract
Magnetic Resonance Imaging (MRI) is an important diagnostic and research tool that provides detailed images of the brain non-invasively. However, it is limited by resolution (approx. 1mm). The development of models that can link features of the image to underlying cellular information at the micrometre scale would significantly improve specificity and sensitivity of diagnosis and help to tailor treatments to individual patients. We aim to develop such a model by directly comparing MRI to three-dimensional microscopy. Then, we will test the framework on a stroke animal model. Stroke is the second cause of death worldwide and produces a complex pattern of brain injury followed by various degrees of cellular regrowth. It is therefore an optimal clinical case to validate our model, leading to the development of accurate and precise imaging-based biomarkers.
The student will engage in specialist training with ex vivo and in vivo (subject to the experience and wishes of the applicant) animal handling, preclinical imaging, and data analysis techniques. The successful candidate will also acquire new computational and modelling skills as well as learn practical laboratory procedures to make a brain transparent. This will allow the student to model features of the MR images using 3D microscopy images.
The student will engage in specialist training with ex vivo and in vivo (subject to the experience and wishes of the applicant) animal handling, preclinical imaging, and data analysis techniques. The successful candidate will also acquire new computational and modelling skills as well as learn practical laboratory procedures to make a brain transparent. This will allow the student to model features of the MR images using 3D microscopy images.
People |
ORCID iD |
| Matteo Bastiani (Primary Supervisor) | |
| Jenna Hanmer (Student) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| MR/N013913/1 | 01/10/2016 | 30/09/2025 | |||
| 2448439 | Studentship | MR/N013913/1 | 01/10/2020 | 31/03/2024 | Jenna Hanmer |
| Description | Participate in Voice of Young Science: Quality and Peer Review workshop |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| URL | https://senseaboutscience.org/voys/#:~:text=VoYS%20is%20a%20unique%20and,media%20view%20science%20an... |
| Description | Flexible funding |
| Amount | £8,660 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2022 |
| End | 02/2023 |
| Title | Use of gadolinium contrast in sample preparation for ex vivo rodent MRI |
| Description | Include 2mM gadolinium contrast in the solutions (PBS and PFA) used to perfuse rats. Then store the skulls in 2mM gadolinium until MRI. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | The use of a contrast-enhancing agent (i.e., gadolinium) in sample preparation leads to an approximately 10-fold decrease in the average T1 time, from approximately 1600ms to 130ms. This allows for quicker repetition times (TRs), thereby shortening overall scan time, whilst also boosting/preserving image quality. For example, the TR of a 3D-RARE acquisition with a Bruker 7T scanner could be reduced by two thirds (5000ms to 1500ms) when gadolinium was used. This shortened the overall scan time by a factor of three (21h43m to 5h56m), whilst maintaining image contrast. Furthermore, the shorter T1 in contrast-perfused samples can be fully exploited with 3D-EPI diffusion MRI, which allows for more flexible TRs than 2D-EPI. Switching to an 3D-EPI diffusion-weighted acquisition with gadolinium-perfused samples scanned on a Bruker 7T system meant that the TR could be reduced by a factor of fifteen (4700ms to 300ms), leading to a 50% boost in image contrast (signal to noise ratio increases from 40.07 to 60.98), whilst also cutting overall scan time by nearly a quarter (13h4m to 10h40m). The reduction in scan duration and improvement in image quality saves time and money. We have also demonstrated that using gadolinium in sample preparation does not impact on tissue clearing, immunostaining or light sheet microscopy. |
| Title | Pipeline for rodent anatomical MRI |
| Description | This is the main script for processing rodent T2 anatomical MRI. It reorients the rodent scan so it matches the SIGMA template, performs 'brain extraction', corrects for distortions caused by the bias field, registers the T2 scan to the template brain, and segments the brain into tissue classes. |
| Type Of Material | Data analysis technique |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Existing neuroimage processing tools have been developed and optimised for human brains and are not easily translatable to rodent datasets. The limited number of tools and processing pipelines dedicated to rodent imaging data are fragmented. There is also no scientific consensus/standardisation, especially in relation to atlases/templates. This automated pipeline helps standardise processing of structural rodent MRI. It also helps to address problems that arise during the conversion of data collected using preclinical scanners (e.g., images not orientated correctly, inconsistencies between ordering of volumes within 4D images and the values within corresponding bval files, etc.) Many of these problems stem from variation in the data architecture used with different software versions (i.e., Paravision 6 versus Paravision 360) and a lack of back-compatibility. |
| URL | https://github.com/SPMIC-UoN/rodent_anat |
| Title | Pipeline for rodent diffusion MRI |
| Description | The dMRI pipeline performs the following steps: skull stripping; registration to anatomical scan and template space; correction of susceptibility-induced distortions, eddy currents and sample motion; identification and correction of outliers; calculation of quality control (QC) measures; and diffusion tensor (DT) model fitting. |
| Type Of Material | Data analysis technique |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | Existing neuroimage processing tools have been developed and optimised for human brains and are not easily translatable to rodent datasets. The limited number of tools and processing pipelines dedicated to rodent imaging data are fragmented. There is also no scientific consensus/standardisation, especially in relation to atlases/templates. This automated pipeline helps standardise processing of diffusion MRI in rodents. It also helps to address problems that arise during the conversion of data collected using preclinical scanners (e.g., images not orientated correctly, inconsistencies between ordering of volumes within 4D images and the values within corresponding bval files, etc.) Many of these problems stem from variation in the data architecture used with different software versions (i.e., Paravision 6 versus Paravision 360) and a lack of back-compatibility. This diffusion pipeline also generates information that has been useful in my efforts to optimise post-mortem rat MRI. For example, the quality control metrics produced by the pipeline demonstrates that the quality of diffusion data is greatest (SNR of b0 volumes = 60.98) when a gadolinium-perfused sample is imaged using a 3D-EPI acquisition, with a short TR (300ms). Conversely, including gadolinium contrast in the sample preparation reduces the quality of diffusion data (SNR of b0 volumes = 3.41) if a 2D-EPI acquisition, with a much longer TR (6000ms), is used. |
| Description | Ex vivo scanning of Huntington's mice |
| Organisation | Cardiff University |
| Department | School of Biosciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have assisted with on-site scanning of the samples and the processing and analysis of the data acquired. |
| Collaborator Contribution | Our collaborators supplied the samples and some funds to cover the cost of the scans. |
| Impact | This collaboration has led us to assess the viability of ex vivo diffusion MRI in mice using the 7T Bruker BioSpec 70/30 scanner. At this point in time, it does not appear that 3D-EPI diffusion MRI scans produce viable data in mice. The level of noise is too high. We are now exploring whether scanning at another facility will be more successful. |
| Start Year | 2020 |
| Description | Hosted visiting scholar |
| Organisation | University of Adelaide |
| Department | Faculty of Health and Medical Science |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Hosted a post-doctoral visitor for 2 weeks. Shared expertise in pre-clinical neuroimage analysis pipelines. Provided assistance in setting up equipment and installation of new tools. |
| Collaborator Contribution | Shared research results. |
| Impact | This researcher has shared their knowledge of surgical models of stroke and the development of novel therapies. We have shared our skills with neuroimaging. |
| Start Year | 2023 |
| Description | Placement at US university for 5 weeks |
| Organisation | Vanderbilt University |
| Department | Medical image Analysis and Statistical Interpretation (MASI) |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We shared several high-resolution (100µm) multi-modal MRI datasets of the rat brain. We also shared two light sheet microscopy datasets, which had been acquired using a novel optical clearing protocol that is highly effective for the rat brain. |
| Collaborator Contribution | Our collaborator shared his experience in validating MRI contrasts using confocal microscopy. He advised us on the best way to align and combine microscopy and MRI datasets. He also assisted with the optimisation of the registration process and quantification of structural similarity after registration. |
| Impact | The work completed at Vanderbilt greatly contributed towards the success of my PhD and will form a chapter of my thesis, focused on building a cross-resolution framework for image registration of 3D microscopy to 3D MRI. The work also contributed to the development of a conference abstract. In addition, we are planning on writing a paper together after my PhD. The overseas fieldwork placement at Vanderbilt University also helped expand my network and broaden my horizons. As I was working with leaders at the interface of imaging and microscopy, the internship was beneficial both for my career development, but also for the reputation of the IMPACT DTP. Working at Vanderbilt allowed me to access additional skills and expertise, which I will benefit from for the remainder of my career. Having some experience of the North American academic environment also makes me better informed about potential opportunities elsewhere (for example, a postdoctoral role overseas). The placement further supported the development of my Interdisciplinary Skills (i.e., applied imaging techniques, microscopy, and image analysis). This has contributed to building a crucial mass of imaging expertise in the UK Midlands (the home of the IMPACT DTP), which is needed to respond to new opportunities. |
| Start Year | 2022 |
| Description | Placement at US university for 5 weeks |
| Organisation | Vanderbilt University |
| Department | Vanderbilt Medical Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We shared several high-resolution (100µm) multi-modal MRI datasets of the rat brain. We also shared two light sheet microscopy datasets, which had been acquired using a novel optical clearing protocol that is highly effective for the rat brain. |
| Collaborator Contribution | Our collaborator shared his experience in validating MRI contrasts using confocal microscopy. He advised us on the best way to align and combine microscopy and MRI datasets. He also assisted with the optimisation of the registration process and quantification of structural similarity after registration. |
| Impact | The work completed at Vanderbilt greatly contributed towards the success of my PhD and will form a chapter of my thesis, focused on building a cross-resolution framework for image registration of 3D microscopy to 3D MRI. The work also contributed to the development of a conference abstract. In addition, we are planning on writing a paper together after my PhD. The overseas fieldwork placement at Vanderbilt University also helped expand my network and broaden my horizons. As I was working with leaders at the interface of imaging and microscopy, the internship was beneficial both for my career development, but also for the reputation of the IMPACT DTP. Working at Vanderbilt allowed me to access additional skills and expertise, which I will benefit from for the remainder of my career. Having some experience of the North American academic environment also makes me better informed about potential opportunities elsewhere (for example, a postdoctoral role overseas). The placement further supported the development of my Interdisciplinary Skills (i.e., applied imaging techniques, microscopy, and image analysis). This has contributed to building a crucial mass of imaging expertise in the UK Midlands (the home of the IMPACT DTP), which is needed to respond to new opportunities. |
| Start Year | 2022 |
| Description | Family Science Show (Nottingham) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Science in the Park is a free, family aimed, science event held at Wollaton Park. The event includes a wide range of exhibitors ready to share about STEM subjects (Science, Technology, Engineering & Maths). It features hands-on activities, guided walks and short talks for all ages. The aim is to make science fun and encourage curiosity in children. My participation and support was recognised by the Universities for Nottingham. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://wollatonhall.org.uk/science-in-the-park/ |
| Description | School Placement (Hucknall) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | 12 primary school students participated in 6 activity sessions, submitting a challenging university-style assignment, which was marked by PhD tutors. Many of the students that took part had no parental history of higher education (58%) and live in deprived areas (42%). Average pupil attendance was 80% and 100% of pupils submitted their final assignment for marking. After the placement one student reported: "Studying with my tutor felt like actually being at university, which was great because it made me want to go to university and to aspire to achieve my dreams. What I learnt and achieved while participating in The Scholars Programme is beyond what I thought possible. I have accomplished much more than I thought I could." |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://thebrilliantclub.org/the-scholars-programme/ |
| Description | School Visit (Nottingham) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | ~40 primary school students participated in a workshop for British Science Week where students said that they found the session, which was focused on Growth of the Human brain, interesting, and that they learnt lots of new information. They also really enjoyed seeing the scans of developing brains. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.britishscienceweek.org/growth-our-theme-for-2022/ |
| Description | Specialist tutoring at school (London) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | This tutoring programme (15 hours) was part of the national catch-up effort following the Covid-19 school closures. It aimed to re-engage and rebuild pupils' confidence in core subjects (mathematics) by working in small groups with a subject expert. The programme was specifically designed to support, stretch and challenge mid-high attaining pupils so that they keep aiming high and are able to access competitive universities. The pupils scored 5.0/7 on the meta-cognition scale at the end of the programme, compared to a national average of 4.5/7. The results of the formative assessments also demonstrated that the pupils made good progress (10% improvement in score) in their understanding of ratio and proportion. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://thebrilliantclub.org/brilliant-tutoring/ |