Avery Pennington Email & Phone Number

Harwell Campus, England, United Kingdom

Development of new research software for bio-image analysis that utilises state-of-the-art techniques such as self-supervised deep learning for volumetric image segmentation.Line management of image segmentation and analysis team at the Rosalind Franklin Institute. Development of image analysis pipelines for team and management of quality assurance and delivery of segmentation data and quantitative analysis.Support and development of existing packages maintained by the Rosalind Franklin Institute, including teaching workshops and giving talks at conferences.Development of new approaches for segmenting and analysing image data in new modalities (such as cryo-FIB/SEM) being developed at the Rosalind Franklin Institute.

Harwell, Oxfordshire, United Kingdom

Developed new version of a 3d volumetric data annotation and segmentation application. The application is a client-server application that allows interactive annotation of image volumes and that enables cloud-based image segmentation to be performed interactively by non-specialists. Developed a CNN-based image analysis pipeline for detecting and measuring objects (viruses) in bio-image volumes.

Dundee, United Kingdom

PhD awarded May 22, 2019. Improved image analysis pipeline with original algorithms for structure extraction using Python (using numpy, pandas, scikit-learn, scikit-image and OpenCV). Extensively tested, and bench-marked the image analysis algorithms and quantitative measurements made by my research pipeline. Analyzed the phenotypic data for biologically relevant results in R.

Birmingham, United Kingdom

Developed image analysis systems for segmentation, classification and measurement of the urban environment, including features such as roads, pavements and residential and commercial property. Designed and implemented application and workflows for machine-learning assisted annotation of geospatial datasets. Worked as part of an agile team to deliver the server-side for a web and mobile application for intelligent route planning.

East Malling

Performed on-site processing of images from a 12 month glasshouse experiment. Ported initial MATLAB pipeline to an open-source Python and OpenCV platform. Developed tools for non-specialists to use to extract data from images. Wrote documentation and provided training to the group of technicians. Worked together with imaging technicians on the 12 months of imaging and image analysis for the glasshouse experiment. This including developing a ground truth data set using both manual and semi-automatic methods of extracting detailed root system geometry

Dundee, United Kingdom

Designed image processing algorithms and a full imaging analysis pipeline, including imaging rig built from low-cost off-the-shelf hardware, for image analysis of the plant roots of large perennials. Utilized MATLAB and Java (ImageJ/Fiji) for prototyping. Worked with a very multi-disciplinary team of supervisors to determine measurement priorities and develop a strategy for incremental prototyping of the pipeline.

Doctor Of Philosophy - Phd, Image Analysis

Plant phenotyping (extraction of morphological traits from images) using machine learning methods.

Bsc Hons (1St), Physics - Astrophysics And Cosmology, First