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Bioinformatics

In cell biology, new approaches to imaging - including high-throughput imaging, super-resolution imaging and high-resolution datasets from 3D models or tissues - generate huge image data sets.

In the past, such images could only be analysed visually, leading to a biased and incomplete set of possible interpretations. 

The Bioinformatics Image Core (BIONIC)  has trained bioinformaticians which link biology with mathematics, image processing, computer science and statistics to develop computational tools for image analysis. We use PerkinElmer Opera and Phenix high-content screening microscopes, ImageJ analysis software and the statistical program R with Bioconductor packages such as CellHTS2,  in monolayer and 3D tissue culture. 

Key methodologies include:

  • Applied image segmentation
  • Thresholding
  • Morphological operations
  • Filtering
  • Feature extractions
  • High-throughput statistical analysis
  • Algorithm development

Selected publications

People

  • Janos Kriston-Vizi (Technology leader)

Resources

Equipment

  • Tyan FT48-B8812 High Performance Barebone System
  • SuperServer 4048B-TR4FT

Complete list of publications

Europe PMC | Pubmed

User policies

BIONIC is potentially accessible to UCL researchers, as well as external users, on a collaboration basis. Please contact Janos Kriston-Vizi for details.

Collaborations

  • Sara Mole (LMCB, UK)
  • Mark Marsh (LMCB, UK)
  • Dan Cutler (LMCB, UK)
  • Rob de Bruin (LMCB, UK)
  • Chris Stefan (LMCB, UK)
  • Antonella Riccio (LMCB, UK)
  • Adolfo Saiardi (LMCB, UK)
  • Alison Lloyd (LMCB, UK)
  • EM Core Facility (LMCB, UK)
  • Sarah Tabrizi (UCL, UK)
  • Daniel Hochhauser (UCL, UK)
  • Derek Hausenloy (UCL, UK)
  • Imre Lengyel (UCL, UK)
  • Ariberto Fassati (UCL, UK)
  • Szabadkai Lab (UCL, UK)
  • Masazumi Tada (UCL, UK)
  • Paola Vergani (UCL, UK)
  • Noursadeghi Lab (UCL, UK)
  • Antony N. Antoniou and David Guiliano (UCL, UK)
  • Towers lab, Richard Miles (UCL, UK
  • Paul Gissen (ICH, UCL, UK)
  • Vania Braga (Imperial College London, UK)
  • Buzz Baum (MRC LMB, UK)
  • Jason Mercer (Birmingham University, UK))
  • Hiroyuki Osada (RIKEN CSRS, Japan) 
  • Hwee Kuan Lee (A-STAR Bioinformatics Institute, Singapore)
  • Gabor Foldes, Sian Harding (Imperial College, UK)

Funding

The Royal Society - International Exchanges award

Teaching

  • CELL0022 Advanced Practical Cell Biology - module Co-Leader
  • CELL0026 Cancer: Cause to Cure - Lecturer
  • CELL0018 Research Techniques in Cell Biology - Lecturer
  • MSc Drug Design - Lecturer