Three case studies of image processing applied to confocal and super-resolution microscopy

Piotr will illustrate how to automate image analysis tasks, avoid errors in image interpretation and ensure analysis reproducibility.
Case studies:
1) Computation of the coverage of neurons by synapses in 2D confocal images,
2) Quantification of the dimensions of micro-vessels in 3D confocal images,
3) Tracking of molecules in E. coli bacteria (super-resolution)

Results of the first two projects demonstrate the need to extended certain studies with super-resolution observations. Piotr will discuss how ONI can help with this extension and multi-modality data analysis integration.
A snapshot of mathematical modelling capabilities will be provided in view of a potential future seminar.

As head of the Data Analyis team at ONI Piotr assists preclinical and basic science researchers with data analysis projects spanning biomedical image/signal analysis, machine learning, bio-fluid mechanics and mathematical physiology.

Piotr developed these core skills during his DPhil in Engineering Science (Dulverton scholar, 2010) at Oxford under Prof. Allison Noble and Prof. Yiannis Ventikos; and an EPSRC Wellcome Trust postdoc at Oxford under Prof. Stephen Payne.

During his Career Development Fellowship in Imaging at Keble (2012-2016) he established several multidisciplinary research teams. The research focused on imaging and modelling the pathophysiology of brain vascular conditions. During this collaborative work he noticed that many biology and clinical teams could increase their output by automating microscopy image analysis tasks or using mathematical models to narrow the scope of experiments. He believed, new imaging and information engineering technology needs to be adopted and developed to make this step possible. To act on these observations and now assist a broader research community he joined Oxford Nanoimaging (Oxford spinout company producing super-resolution microscopes to lead their data analysis effort.

He is the lead or corresponding author of 10 journal publications in biomedical engineering.