|Welcome To Flicker|
Of course Flicker might be useful for comparing other types of images such as 2D-blots, 1D gels, serial microscope sections, time-lapse, microarrays, etc. - any type of image where there are distortions or intensity variation of the images, differing numbers of spots, and other systematic and procedural experimental differences. It can read black and white or color JPEG and GIF images, and black and white TIFF images (some un-banded color TIFF images are available).
The Flicker application is Java program that runs under the MS Windows, MacOS-X, Linux and Solaris operating systems. It is downloaded to and runs on your computer. Flicker has been made open source and was contributed to the Open2Dprot project. Both the executable binary as well as the source code is available.
The original version of Flicker was a Java applet that ran in your Web browser ([Lemkin97a]-[Lemkin97c], [Lemkin99], [Lemkin02]) and is available at http://www.ccrnp.ncifcrf.gov/flicker. However, being a Java applet, it had many limitations in its capabilities. To resolve these limitations it was converted in 2003 to a Java application by Peter Lemkin and Greg Thornwall with help from Jai Evans. Code was added from the open-source MicroArray Explorer program, http://maexplorer.sourceforge.net/, to implement some of the new features in Flicker. The new version of Flicker is much more flexible and makes it easier for you to compare your gels with each other or with reference gels on Internet databases. A limited measurement functionality is available to estimate spot or region quantification.
The new version is described in a book chapter Comparing 2-D Electrophoretic Gels Across Internet Databases, PF Lemkin, GC Thornwall, J Evans (2005) in "The Proteomics Handbook", JM Walker (Ed), Humana Press Inc, Totowa, NJ, pp 279-305.
Notice: some individuals have problems looking at flickering imagesSome individuals have problems with flickering images. The Flicker program allows you to flicker-compare two images at flicker rates of 0.1 second/frame up to 3 seconds/frame (individually selected on a per-image basis). If you are bothered by flickering images, do not download this program or do not use the flicker image comparison option. However, the program can be used without flicker and may still be useful to zoom/dezoom images, adjust brightness/contrast, do image transforms, identify and label spots via comparison with SWISS-2DPROT images, etc. In this case, don't enable the flicker option.
Quick start examples
A. Compare two gels to find spot differences.
B. Compare your gel against an Internet reference gel to try to putatively identify the spot.
C. Quantitate a list of spots. Flicker has a rudimentary spot list definition and quantification capability that might be used as follows:
D. Putatively identify a list of spots in your gel that are identified in an active reference gel by first identifying spots in the reference gel and then using them to identify corresponding spots in your gel.
Use of 2D-PAGE in modern proteomics
This approach may be useful for comparing similar protein samples
created in different laboratories to help putatively identify or
suggest possible protein spot identifications. The gels should be run
under similar pH and molecular weight ranges if possible. Although
available for over three decades, 2D polyacrylamide gel
electrophoresis (2D-PAGE) is still routinely used  even considering the now common
use of mass spectrometry [2-7]
and recently protein arrays 
for protein identification. If you have defined a list of spots in an
active gel (such as one of the Swiss-2DPAGE gels) and you are
connected to the Internet, you can request Flicker to lookup the
annotation information (Swiss-Prot id and name) for each spot in the
list. Then you can define a list of spots in your gel that correspond
to spots in the annotated active reference gel, and then assign these
protein identifications to your gel.
Recent advances, such as IEF "zoom" fractionation gels  that divide the protein sample by pH range or immunoaffinity subtraction with LC , greatly increase the resolution and numbers of spots able to be discriminated by subsequent 2D-gel electrophoresis. Another increasingly common image comparison technique uses 2 to 6 cyanine dyes using dye multiplexing to label multiple control and experimental samples run in the same gel such as DIGE  and scanned with very high resolution systems . Multiple scans of the same gel using different color filters can then be color mapped to see the contributions of the different samples. This is useful if one has control over the experimental design when determining the reference gel, set of control gels, and experimental gels. However, it does not solve the problem of trying to putatively compare one's own sample against an Internet reference gel where they have identified protein spots.
Finding reference gels on the Internet
A number of 2D-gel image databases are available on the Web where some
of the proteins are identified for various types of samples. Both WORLD-2DPAGE and
the SWISS-2DPAGE [12-15] server can be used to find
Web URL addresses for a number of 2D protein gel databases. The Web
site a large number of tissues with databases that include a wide
range of human tissues, mouse tissues, E. coli,
aribidopsis, dictyostelium, and yeast. You might also
try a Google
Active 2D image maps in Internet 2D-gel databases
Some 2D-gel image Web databases have active maps (e.g., SWISS-2DPAGE)
where you can click on a
spot in an active gel image to identify the protein if it is in
their database (see WORLD-2DPAGE). Clicking
on a spot queries the associated Web server database to determine if
the spot you pointed to is in that database. If it is, it then
reports the protein identity of the spot with links to SWISS-PROT
etc. Alternatively, you can have it report the ID and protein name in
the reporting window or assign it to the selected spots annotation.
Flicker was developed to fill the need for a quick comparison of a researcher's gel image against one of these internet reference 2D-gels. We have also provided a limited quantification facility for manually measuring, annotating, a limited number of spots.
The Flicker Reference Manual describes the operation of the various commands. The current status of the program and the revision history is updated as changes occur in the software. You download the software to install it on your computer. Flicker is downloaded as a Zip file from the Files Mirror.
Please contact us with suggestions and comments. If you make interesting changes in the source code, please send us a copy and describe your changes so we can merge them in the released version.
|Contact us||Flicker is a contributed program available at