CoLocalizer Pro

CoLocalizer Pro
CoLocalizerPro press.png
CoLocalizerPro Screenshot under MacOSX 10.6 SnowLeopard.png
Screenshot of CoLocalizer Pro 2.6 with the main application window, background correction, histogram, and colocalization windows
Developer(s) CoLocalization Research Software
Initial release April 23, 2004 (2004-04-23)
Stable release 2.6.1 / January 21, 2011; 9 months ago (2011-01-21)
Operating system Mac OS X 10.5 (Leopard) and newer
Platform Apple Macintosh
License Commercial; free evaluation trial available
Website www.colocalizer.com

CoLocalizer Pro is a scientific software application, developed by CoLocalization Research Software, that allows researchers to analyze colocalization in the images obtained using fluorescence microscopy. Due to high popularity of Macintosh computers in medicine and biology, the software is designed specifically for Mac OS X operating system.[1] To bring the full advantage of Mac OS X, it is written exclusively in Cocoa. The software is a Universal application with both Intel and PowerPC compatibility. CoLocalizer Pro is used in universities and research institutions worldwide. Lite version of the software, CoLocalizer Express, is geared toward students and beginners.

In October 2011 issue, renown Nature Protocols published a CoLocalizer Pro-based protocol to quantify spatial correlations of fluorescent markers.[2] The protocol described in details the steps needed to be taken to perform quantification of colocalization of synergetic proteins.

Contents

Overview

CoLocalizer Pro estimates the degree of colocalization by calculating several specialized coefficients and prepares obtained results for presentation and publication. The following coefficients can be calculated: Pearson's correlation coefficient (Rr), overlap coefficient (R), overlap coefficients k1-k2, colocalization coefficients m1-m2, and colocalization coefficients M1-M2.[3] The workflow is designed to ensure that the results are accurate and reproducible.[4] To provide the accuracy, the image background noise is corrected (removed) prior to the analysis and therefore does not impact the results. The information about the degree of colocalization of proteins can play a role in understanding their functional significance with various medical and biological implications.[5][6][7][8][9][10][11][12][13][14][15][16]

Features

  • Compatible with images created by all major brands of fluorescence microscopes
  • All calculations can be performed without the need to be connected to a microscope
  • Unique background correction tools guarantee reliability of quantification
  • Calculates coefficients on the image's and scatter gram's regions of interest (ROI)
  • Reveals colocalized and selected on the scatter gram ROI pixels, traces pixels of a particular color
  • Exports data in various file formats, such as Microsoft Excel, Text, PDF, and HTML
  • Integrated with iLife software suite

CoLocalizer Pro is currently at version 2.6.1 and is continued to be developed by the CoLocalization Research Software team. The software capitalizes on its strength in the implementation of the background correction functionality. Its another notable feature is the option to save the results of coefficients calculations and image analysis as session reports with all the data combined in a single file for compact storage and further reference.

References

  1. ^ MacResearch "Showcase: Affordable Quantitative Colocalization Analysis with CoLocalizer Pro."
  2. ^ Zinchuk V et al (2011). "Quantifying spatial correlations of fluorescent markers using enhanced background reduction with protein proximity index and correlation coefficient estimations." Nat Protoc 6:1554-1567.
  3. ^ Zinchuk V et al (2007). "Quantitative colocalization analysis of multicolor confocal immunofluorescence microscopy images: pushing pixels to explore biological phenomena." Acta Histochem Cytochem 40:101-111.
  4. ^ Curr Protoc Cell Biol "Quantitative colocalization analysis of confocal fluorescence microscopy images."
  5. ^ Van Acker GJ et al (2007). "Cause-effect relationships between zymogen activation and other early events in secretagogue-induced acute pancreatitis." Am J Physiol Gastrointest Liver Physiol 292:G1738-G1746.
  6. ^ Watanabe T et al (2007). "Involvement of host cellular multivesicular body functions in hepatitis B virus budding." PNAS 104:10205-10210.
  7. ^ Marinkovic D et al (2007). "Foxo3 is required for the regulation of oxidative stress in erythropoiesis." J Clin Invest 117:2133-2144.
  8. ^ Hayashida T et al (2007). "MAP-kinase activity necessary for TGFβ1-stimulated mesangial cell type I collagen expression resuired adhesion-dependent phosphorylation of FAK tyrosine 397." J Cell Sci 120:4230-4240.
  9. ^ Yoshizawa T et al (2009). "Role of MAPK kinase 6 in arthritis: distinct mechanism of action in inflammation and cytokine expression." J Immunol 183:1360-1367.
  10. ^ Leffler J et al (2010). "Annexin-II, DNA, and histones serve as factor H ligands on the surface of apoptotic cells." J Biol Chem 285:3766-3776.
  11. ^ Boileau AJ et al (2010). "The short splice variant of the γ2 subunit acts as an external modulator of GABAA receptor function." J Neurosci 30:4895-4903.
  12. ^ Krementsov D et al (2010) "HIV-1 assembly differentially alters dynamics and partitioning of tetraspanins and Raft components." Traffic 11:1401-1414.
  13. ^ Kuipers MA et al (2011). "Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload." J Cell Biol 129:29-41.
  14. ^ Delputte PL et al (2011). "Porcine sialoadhesin (CD169/Siglec-1) is an endocytic receptor that allows targeted delivery of toxins and antigens to macrophages." PLoS One 6-e16827.
  15. ^ Palatinus JA et al (2011). "ZO-1 determines adherens and gap junction localization at intercalated disks." Am J Physiol 300:H583-594.
  16. ^ Baumann C et al (2011). "Chromatin configuration and epigenetic landscape at the sex chromosome bivalent during equine spermatogenesis." Chromosoma 120:227-244.


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