Bioinformatics Image Core BIONIC

LMCB Bioinformatics Image Core cell biology image processing image analysis bioinformatics MRC UCL high-content analysis high throughput screening high-content screeningManager: Dr. Janos Kriston-Vizi

 

 

 

The Bioinformatics Image Core provides services for researchers from various areas in cell biology and analysis of large data sets from high-throughput screening experiments.

 

The Bioinformatics Image Core (BIONIC) facility supports:

 

  • the high-throughput screening activities at the Translational Research Resource Centre
  • the image processing and data analysis throughout the LMCB

 

 

 

Advanced microscopic technology is allowing imaging approaches to detect cellular dynamics with increasing spatial and temporal resolution. New approaches are required to allow effective analysis and quantitation of the data, requiring individuals with advanced skills in image analysis and computing.

 

 The core facility has experience in image analysis, statistical methods for analyzing large data sets and experience in automation processes. as well as a good understanding of genomic technologies and the drug discovery process. We have experience in operation of PerkinElmer Opera high-content screening microscope. The core's activity is based on image analysis softwares ImageJ and Acapella as well as the statistical program R with Bioconductor packages such as CellHTS2. Furthermore, we have some experience in tissue culture and basic laboratory techniques.

 

Equipment of the Bioinformatics Image Core

 

 

 

 
ASUS Server Z8PE-D18
144 GB memory
2x Quad-Core Intel® Xeon® E5520 CPUs (16 cores)
Corsair Hydro H50 High Performance Liquid  CPU Cooler
NVidia Quadro FX3800
Linux
 

 

 

 

 

 

 
Tyan FT48-B8812 High Performance Barebone System
256 GB memory
4x 12-Core AMD® Opteron® 6174 CPUs (48 cores)
NVidia GeForce GTX 580
Acer GN245HQ 3D monitor with NVidia 3D Vision
Linux

 

 

 

 
 
Ultima 9550i Tyrannosaur MKIII
Intel Core i7 3770K 3.50GHz @ 4.60GHz 8-Core
DDR3 32GB Ivybridge
Nvidia GTX 680 
Asus VG278H 3D monitor with NVidia 3D Vision 2

 

 

 

SuperMicro 4048B TR4FT Kriston-Vizi LMCB UCL
SuperServer 4048B-TR4FT
4x Intel Xeon E7 4809 v2.0 @ 1.9 GHz 8-Core
DDR4 1TB (32x32GB 2133MHz)
AMD Radeon R9 290 (4GB)
 

 

 

UCL Drug Design - Phenotypic Screening course supporting files

 

ImageJ/Fiji Cell Outliner plugin compiled files.

 

- Download Cell_Outliner.png and copy into Imagej/Fiji "Plugins" folder.

 

- Rename the file extension from .png to .jar

 

- Start ImageJ/Fiji.

 

 

 

Janos Kriston-Vizi Orcid QR code

 

Selected Publications

 

 

 

Ferraro F , Mafalda Lopes da S , Grimes W , Lee HK , Ketteler R , Kriston-Vizi J , Cutler DF (2016) Weibel-Palade body size modulates the adhesive activity of its von Willebrand Factor cargo in cultured endothelial cells. Sci Rep (PMID:27576551)

 

 

 

 

Prak, K., Kriston-Vizi, J., Chan, A. W., Luft, C., Costa, J. R., Pengo, N., & Ketteler, R. (2015). Benzobisthiazoles Represent a Novel Scaffold for Kinase Inhibitors of CLK Family Members. Biochemistry.

Prak, K., Naka, M., Tandang-Silvas, M. R. G., Kriston-Vizi, J., Maruyama, N., & Utsumi, S. (2015). Polypeptide modification: An improved proglycinin design to stabilise oil-in-water emulsions. Protein Engineering, Design and Selection, 28 (9), 281-291. doi:10.1093/protein/gzv031

Rodrigues, N. T., Lekomtsev, S., Jananji, S., Kriston-Vizi, J., Hickson, G. R., & Baum, B. (2015). Kinetochore-localized PP1-Sds22 couples chromosome segregation to polar relaxation. Nature, 524 (7566), 489-492. doi:10.1038/nature14496

Ferraro F, Kriston-Vizi J, Metcalf DJ, Martin-Martin B, Freeman J, Burden JJ, Westmoreland D, Dyer CE, Knight AE, Ketteler R, Cutler DF (2014) A Two-Tier Golgi-Based Control of Organelle Size Underpins the Functional Plasticity of Endothelial Cells. Developmental Cell. 29 (3), 292-304.

Stevenson NL, Martin-Martin B, Freeman J, Kriston-Vizi J, Ketteler R, Cutler DF (2014) G protein-coupled receptor kinase 2 moderates recruitment of THP-1 cells to the endothelium by limiting histamine-invoked Weibel-Palade body exocytosis. Journal of Thrombosis and Haemostasis. 12 (2), 261-272.

Foldes G, Matsa E, Kriston-Vizi J, Leja T, Amisten S, Kolker L, Mioulane M, Vauchez K, Aranyi T, Ketteler R, Schneider M, Denning C, Harding S (2013) Key differences in hypertrophic signalling in hESC-and hIPSC-derived cardiomyocytes. Human Gene Therapy. 24: A9-A9.

Kriston-Vizi, J. (2013, June 28). High Content Imaging at LMCB. Computational Life and Medical Sciences (CLMS) Annual Symposium. University College London, UK. http://www.clms.ucl.ac.uk/node/254

Kriston-Vizi, J. (2013, June 6-7). 3D and 2D cellular high-content screens identify novel autophagy regulator kinase inhibitors.  European Lab Automation 2013, Drug Discovery Automation: High-content Screening & Cell Based Assays. Hamburg, Germany. http://selectbiosciences.com/conferences/index.aspx?conf=DDAHCS2013

Barry, D., Roque, H., Dumoux, M., Kriston-Vizi, J., Bodea, G. and Harper, C. (2013). Meeting Report – Imaging in Cell Biology: Where Next? Journal of Cell Science 126 (1), 43-44.

Kriston-Vizi, J., Ketteler, R. (2012, February 4). Single-Cell Volume Determination for 3D Segmentation of Human Cancer and Nontumourigenic Cells to Identify Autophagic Phenotypes in High-Content Screening. SLAS2012 Society for Laboratory Automation & Screening. San Diego, USA.

Evans, R., Coussens, A. K., Kriston-Vizi, J., Chain, B. J., & Noursadeghi, M. (2011). The effect of vitamin D on monocyte biology: a physiological perspective. In IMMUNOLOGY Vol. 135 (pp. 88). Retrieved from http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000297507100254&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=f41074198c063036414efcbc916f8956

Freeman, J., Kriston-Vizi, J., Lindenschmidt, I., Haider, M., & Ketteler, R. (2011). Autophagy protease ATG4B as a target in drug discovery. INT J MOL MED, 28, S72.

Kriston-Vizi, J. (2011, November 17). From image processing to hits: a high-content analysis pipeline using free software. In 16th Academic Screening Group Meeting. Sutton, UK.

Kriston-Vizi, J., Wee Thong, N., Leong Poh, C., Chia Yee, K., Poh Ling, J. S., Kraut, R., Wasser, M. (2011). Gebiss: An ImageJ Plugin for the Specification of Ground Truth and the Performance Evaluation of 3D Segmentation Algorithms. BMC Bioinformatics, 12, 232. doi:10.1186/1471-2105-12-232

Kriston-Vizi, J., Ching Aeng, L., Condron, P., Chua, K., Wasser, M., & Flotow, H. (2010). An Automated High-Content Screening Image Analysis Pipeline for the Identification of Selective Autophagic Inducers in Human Cancer Cell Lines. Journal of Biomolecular Screening, 15(7), 869-881. doi:10.1177/1087057110373393