Bioinformatics Image Core BIONIC

Manager: Dr. Janos Kriston-Vizi

Janos Kriston-Vizi Marie Curie grant LMCB Bioinformatics Image Core cell biology image processing image analysis bioinformatics MRC UCL high-content analysis high throughput screening high-content screening

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 CBU/LMCB

 

LMCB Bioinformatics Image Core cell biology image processing image analysis bioinformatics MRC UCL high-content analysis high throughput screening high-content screening

 

 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

 

LMCB Bioinformatics Image Core cell biology image processing image analysis bioinformatics MRC UCL high-content analysis high throughput screening high-content screening
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
LMCB Bioinformatics Image Core cell biology image processing image analysis bioinformatics MRC UCL high-content analysis high throughput screening high-content screening

 

 

LMCB Bioinformatics Image Core cell biology image processing image analysis bioinformatics MRC UCL high-content analysis high throughput screening high-content screening
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

 

LMCB Bioinformatics Image Core cell biology image processing image analysis bioinformatics MRC UCL high-content analysis 

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

 

Selected Publications

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

Rambabu,
C., Choo, P. W., Kriston-Vizi, J., & Waser, M. (2009). 3D
segmentation for the study of cell cycle progression in live
drosophila embryos.
Proceedings
of the 1st International Workshop on Medical Image Analysis and
Description for Diagnosis Systems, MIAD 2009 in Conjunction with
BIOSTEC 2009
,
43-51.

Kriston-Vizi,
J., Umeda, M., & Miyamoto, K. (2008). Assessment of the water
status of mandarin and peach canopies using visible multispectral
imagery.
Biosystems
Engineering
,
100(3),
338-345.