My principle role is to support users of the Centre for Cell Imaging at the University of Liverpool. This job involves everything from experimental design through advanced imaging techniques to post-acquisition analysis and workflow development. Furthermore I oversee parts of the IT infrastructure at the CCI including the fileservers, computing workstations, our online booking system and web application servers (more details below). My position is currently funded through cost-recovery by the facility and the Technology Directorate.
I completed my PhD in Toronto under the supervision of Sergio Grinstein at the Hospital for Sick Children. My main area of study was the modulation of Actin and Lipids during phagocytosis and during bacterial Host-Pathogen interactions. During this time, I acquired a lot of hands-on experience with light microscopy which has driven my research interests ever since.
I returned to the UK to take up a Marie Curie International Incoming Fellowship (IIF) at the University of Birmingham studying bacterial adhesion using fast 4D acquisition and post-acquisition tracking. I joined the Lévy Group at the University of Liverpool in March 2014 on an MRC Next Generation Optical Imaging Initiative and have since been expanding my experience with Light Microscopy and developing my role as a BioImage Analyst.
Skills and Interests
Research in Cell Biology and Microbiology
I have many years experience in Cell Biology including 2D and 3D culture systems and manipulation of those systems through electroporation, microinjection and transfection. I am also trained as a microbiologist (largely gram negative organisms) with the majority of my work being with Salmonella enterica.
Advanced Light Microscopy
I have practical experience using and training others with widefield, TIR-FM, photothermal and confocal microscopy (laser scanning and Nipkow Spinning Disk). I have special interest in low-light and/or high-speed applications and have a basic working knowledge of Atomic Force Microscopy.
Image and Data Analysis
My current role supporting the Centre for Cell Imaging means a lot of interaction with users discussing or developing bespoke Image Analysis solutions. I'm well versed in many open and closed-source tools and do most of my image analysis work with Fiji. For segmentation, tracking and rendering of 3D+ datasets, I usually use Trackmate or Imaris. My tool of choice for data analysis is MATLAB. I have worked on hundreds of projects including segmentation and classification (basic and through machine learning), tracking, object and intensity based localisation and automation of workflows.
Teaching, Training and Outreach Activities
I enjoy teaching and training, especially in topics such as digital imaging theory, image analysis and post-acquisition processing, which is the topic of my blog. I am available to train individual users, lab or working groups or provide guided workshops, seminars and talks.
IT & Infrastructure
Any high-end facility requires good IT support and infrastructure. I have been involved in the design, deployment and maintenance of our file-management offerings at the CCI. This involves management of user and group permissions as well as quota allocation, backups and monitoring. I also have a good working understanding of virtual machines as development and testbed servers.
I am highly proficient in Windows, recent OS-X/macOS and several flavours of headless GNU/Linux on which our file and application servers run. I have been responsible for deploying and maintaining several application servers including BookedScheduler for CCI bookings, OMERO for research data management, Zegami to use as a visualisation platform and a local Worpress server for use as an ELN for research groups. I have a good knowledge of HTML/CSS/JS and have written and maintain several websites.
I have always loved taking things apart to study or fix them. These days, I'm pretty good at CAD prototyping and fabrication in a range of materials, 3D printing, soldering and generally MacGyvering my way (into and) out of situations.
Below are a few exemplar projects I've worked on with CCI users. Please get in touch for more details.
The location of many proteins and organelles in the cell dictate their function or activity. By studying where the protein (in this case GLUT4) spatially localises in various conditions can help us to better understand how a protein is regulated in these conditions. In this example, a DNA stain was used to demark the location of a nucleus (A) then a perinuclear region was created based on this selection (B). Intensity was measured and a ratio was calculated based on the whole cell fluorescence (C). By taking ratios to normalise the signal, cells with different staining levels and even from different experiments can be compared.
Tracking Cells in Spheroid Cultures
Many cancers form as solid tumours. Understanding how these 'spheroids' form and grow can help to better our understanding of cancer progression and metastasis, but this is not an easy endeavour. Imaging and analysing 3D cell cultures over time takes expertise and experience. Below, a spheroid culture (~0.5mm diameter) was imaged using a lightsheet microscope.
Some of the cells were genetically encoded with a nuclear marker (H2B-RFP) and tracked over 24 hours. By following individual cells, physical parameters such as speed and spatial distribution can be calculated.
Volume and spot segmentation in Drosophila brains
The fruit flies of the Drosophila species are a commonly used model organism in developmental research. Whole or disected organisms can be imaged using a range of techniques. Below, as part of a study into glial tumours, the effect of the MRL protein pico on oncogenesis was studied.
To characterise the effects, the original stack (A) was segmented using the GFP-positive lobes. This allowed for labelled cells of interest to be segmented, counted and measured (B). The analysis was performed using Bitplane Imaris.
The wound healing assay is a fairly common technique in the Cell Biology Research toolkit. The idea is simple: grow cells to cover a surface, scratch a ‘wound’ into the cells then see how well the cells can close the wound (either by replication, migration or a combination of both).
A number of metrics can be used to characterise the rate of wound healing, including wound width or fractional wound closure. It's important to keep in mind what you're trying to measure as often, tracking the migration of individual cells (below, A) can provide the same (or more) information including Speed, Straightness and Directionality (below B,C).
Get in touch
Office G26, BioSciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
+44 (0)1517 954454