Microscopic Image Analysis for Cell Biology

Lead Research Organisation: University of Dundee
Department Name: School of Computing


Advances in microscopy technology are enabling cell biologists to design experiments which generate very large numbers of images of interesting biological phenomena. These images are sometimes two-dimensional but are often in three dimensions and are acquired over time, like 3D video. Such images need to be studied and analysed so that the results of the experiments can be interpreted. This is very labour intensive so there is a growing need for computer software that can analyse the images automatically. This is challenging because the images are highly variable even within a single type of experiment. Images also vary in scale from images taken of activity within a single cell to image sequences of entire moving populations of cells. In this project, computer scientists specialising in developing software to analyse images will work with life scientists to develop this automation. They will make use of recent developments in computer vision and machine learning which enable computers to learn from examples how to interpret images. Several lines of collaboration will be explored with an initial focus on analysing images of cell-based assays obtain using fluorescence microscopy. Software developed will be made available to researchers via a large open software project called OMERO.

Technical Summary

Researchers from Computing will ?hop? discipline to the Life Sciences to initiate collaboration on automated image analysis for cell biology. Requirements for microscopy image analysis have shifted dramatically in recent years as technology developments have enabled higher throughput and higher resolution multi-dimensional, multi-spectral data sets to be routinely acquired, often at multiple scales. Algorithms that automate analysis of cell biology images are crucial as manual annotation of such data is often the rate-limiting step in microscopy workflow. The large data sets generated by high-throughput techniques enable modern machine learning methods to be leveraged: algorithms that scale well to large image data sets in which only relatively small numbers of images are partially annotated. Initial activity will focus on analysis of phenotypes from fluorescence microscopy images of in vivo cell-based assays. Software developed will be integrated and disseminated via the open OMERO project.


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McKenna S (2012) Special issue on microscopy image analysis for biomedical applications in Machine Vision and Applications

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Wang R (2011) Recognition of immunogold markers in electron micrographs. in Journal of structural biology

Title ImmunoEM 
Description Software for automatic localisation of immunogold markers in immunoelectron microscopy. 
Type Of Material Data analysis technique 
Provided To Others? No  
Impact Recognition of immunogold markers in electron micrographs. Wang R, Pokhariya H, McKenna SJ, Lucocq J. J Struct Biol. 2011 Nov;176(2):151-8. 
Description JL 
Organisation University of St Andrews
Department School of Medicine St Andrews
Country United Kingdom 
Sector Academic/University 
PI Contribution Development of algorithms and software for automatic analysis of immunoelectron micrographs.
Collaborator Contribution Joint publication and joint grant proposal submissions
Impact It is interdisciplinary (Electron microscopy/cell biology and computing/image analysis). Recognition of immunogold markers in electron micrographs. Wang R, Pokhariya H, McKenna SJ, Lucocq J. J Struct Biol. 2011 Nov;176(2):151-8.
Start Year 2010
Description KW 
Organisation University of Dundee
Department College of Life Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-supervision of PhD studentship on image analysis of epithelial sheets.
Collaborator Contribution Supervision of PhD studentship on image analysis of epithelial sheets.
Impact No outcomes yet
Start Year 2011
Description Presentation at workshop for industry stakeholders 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact A workshop held at University of Lincoln was to present findings to industry stakeholders on potential technologies for automated meat
inspection, targeted specifically at issues relating to public health on red meat and poultry.
Year(s) Of Engagement Activity 2017