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Informatics service support for health and biomedical research at the University of Bristol

Stephen Cross

Dr Stephen Cross

David Lee

Dr David Lee

7 June 2017

The Elizabeth Blackwell Institute for Health Research (EBI), through its Wellcome Trust ISSF Award, and match funded by the University of Bristol, invested in two posts that are openly available to help support all health and biomedical researchers across the University in their informatics needs.

Dr Stephen Cross, Research Associate in Microscopy Image Processing and Analysis, Wolfson Bioimaging Facility, and Dr David Lee, Research Associate in Bioinformatics, Life Sciences, explain the support and expertise they offer.

Dr Stephen Cross:
The primary purpose of my role is to assist users with processing and analysis of microscopy images; typical examples of which include 3D segmentation of cells, characterisation of protein colocalisation using the overlap of fluorescent signals and tracking cells and measuring their mobility.  Since starting I provided assistance on approximately 70 projects covering a variety of biomedical disciplines.  For some projects, my involvement has been as simple as demonstrating and training users in image analysis software packages such as ImageJ/Fiji and CellProfiler but some problems require more complex image processing and analysis. 

Where the proposed analyses haven’t been possible using existing software, I’ve been developing novel solutions.  These take a variety of forms, including development of ImageJ/Fiji macros and plugins, addition of functionality to CellProfiler or creation of analysis packages in MATLAB.  One recent example is the development of a workflow to batch analyse 3D image stacks created by high content microscope systems.  Each image stack contains fluorescently-labelled cells, which need to be segmented in 3D, then various shape, orientation, spatial distribution and protein (indicated by fluorescence) distribution measurements to be taken.  Since high content microscopes can create hundreds or thousands of such stacks for samples held in a 96-well plate, the analysis must keep track of their location and individual measurements, then export these in a manageable way (i.e. as a single spreadsheet).

I have also been co-running workshops: an introductory-level session covering use of ImageJ/Fiji and an advanced course focussing on macro writing and analysis automation.  These are typically run every 6 months and can be booked via the University of Bristol OnCourse system.

Please contact me at or on 0117 33 12142 (ext 12142) to discuss your project and to see how I can help with processing and analysis of your microscopy images.

‌Dr David Lee:
I have been working in bioinformatics since completing my PhD in 1999 in molecular dynamic simulations at Birkbeck College, University of London. Much of my work in the past has been in structural bioinformatics at University College London, analysing, predicting and comparing the structures and functions of proteins. More recently, I have expanded my expertise at Bristol into transcriptomics, proteomics and statistics and can now assist with truly comprehensive analyses.

Do you need help designing and analysing a deep sequencing experiment, or the output of a qualitative proteomic experiment (e.g. SILAC, iTRAQ etc)? Are you struggling with an unfamiliar file format? Can’t get a computer program or web server to work on your genomic or proteomic dataset? Not sure how to handle terabytes of output from such an experiment or whether your results are statistically significant or not?  I will be happy to help!

Please contact me at or on 0117 39 41420 (ext 41420) to discuss how I could collaborate with you on your project.

Further information

If you have any suggestions or comments about bioinformatics support for health and biomedical researchers at the University of Bristol please contact Dr Nina Couzin, Institute Manager, Elizabeth Blackwell Institute, at or on 0117 42 82483 (ext 82483).

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