CoLocalizer Pro

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CoLocalizer Pro
CoLocalizerPro press.png
CoLocalizerPro Screenshot under MacOSX 10.6 SnowLeopard.png
Screenshot of CoLocalizer Pro 2.7.1 running under Mac OS X 10.8 Mountain Lion
Developer(s) CoLocalization Research Software
Initial release April 23, 2004 (2004-04-23)
Stable release 2.7.2 / February 3, 2014; 6 months ago (2014-02-03)
Development status Active
Written in Cocoa
Operating system Mac OS X 10.6.6 Snow Leopard and newer
Platform Apple Macintosh
Type Application Software
License Proprietary; 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, it is designed specifically for Mac OS X operating system.[1] To bring the full advantage of Mac OS X, the software is written exclusively in Cocoa. CoLocalizer Pro is used in universities and research institutions worldwide. Lite version of the software, CoLocalizer Express, is geared toward students and beginners.

The use of CoLocalizer Pro software is cited by various top impact factor journals, including Cell, Nature Neuroscience, Nature Methods, Journal of Clinical Investigation, Journal of Cell Biology, PNAS, etc. 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.

Overview[edit]

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 of calculations, the image background noise is corrected prior to the analysis and therefore does not impact the results. Another notable feature of the software 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. 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][17][18][19]

Features[edit]

  • 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

Free colocalization benchmark sets[edit]

Quantitative data obtained using CoLocalizer Pro can be validated with the help of free downloadable image sets from the Colocalization Benchmark Source. By calculating and comparing the values of coefficients on their images versus benchmark images from CBS, researchers can interpret their calculations.

References[edit]

  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. ^ Palatinus JA et al (2011). "ZO-1 determines adherens and gap junction localization at intercalated disks." Am J Physiol 300:H583-594.
  15. ^ Yang L et al (2011). "ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs." Cell 147:773-788.
  16. ^ Shen Z et al (2012). "An artery-specific fluorescent dye for studying neurovascular coupling." Nat Methods 9:273-276.
  17. ^ Zinchuk V et al (2013). "Bridging the gap between qualitative and quantitative colocalization results in fluorescence microscopy studies." Sci Rep 3:1365 doi:10.1038/srep01365.
  18. ^ Burchell VS et al (2013). "The Parkinson’s disease genes Fbxo7 and Parkin interact to mediate mitophagy." Nat Neurosci 16:1257-1265.
  19. ^ Kazi JU et al (2014). "Src-Like adaptor protein (SLAP) differentially regulates normal and oncogenic c-Kit signaling." J Cell Sci 127:653-662.


External links[edit]