Seg2Dgel - 2D electrophoresis gel spot segmenter

Seg2Dgel - 2D electrophoresis gel spot segmenter

Welcome To Seg2Dgel

http://open2dprot.sourceforge.net/Seg2Dgel and
(http://www.lecb.ncifcrf.gov/Open2Dprot/Seg2Dgel/ mirror)


Note: This pre-alpha level software is under construction and will change. 
Not all functionality described is fully implemented or fully debugged.    
This documentation will undergo revision as the program develops.  

Introduction

Seg2Dgel is a Java 2D-electrophoretic gel segmentation program for finding and measuring the integrated density and position of spots in a gel or image with similar types of data. We are enhancing it to segment spots in 2D LC-MS images. It is a step [2] module in the pipeline analysis for the Open2Dprot project. The segmentation is performed on a computing window region of interest (ROI) of a 2D gel image file. It uses the second derivative (laplacian) magnitude and direction of the gaussian-smoothed gel image as well as neighborhood connectivity properties in determining spot extents. It can handle grayscale TIFF, JPEG and GIF images. It generates a spot list of segmented spots which is saved in a Sample Spot-list File (SSF) in a variety of file formats (XML, tab-delimited, and human readable text).

The program may be run either interactively (-gui) with a graphical user interface (popup Report Window GUI) or under an OS shell command to implement batch (-nogui). If the demonstration switch is set(the default) to (-demo ), it defaults to demonstration mode for some sample gels supplied with the distribution. Add the -nodemo switch to disable demo mode.

In the former GUI case (-gui), after the segmentation is finished, the user has the option of interactively viewing any of the images used by the segmenter and querying them for quantified spot data to look at small pixel windows (3x3 to 21x21 pixels) of the image data, or analyze the image or spot list data with dynamic histograms that allow limited data filtering. The latter is useful for titrating threshold sizing parameters. This is done using the Image Viewer window. The user may then modify the input switch options using the Command Options Wizard window and save the new options in a "Seg2Dgel.properties" file in the current project directory so that it may be used as the default switch options in subsequent running of the segmenter.

You can currently download the pre-alpha version and install it on your computer. Currently, Seg2Dgel is hardwired to start with the demo gel and with the -gui switch. The remainder of this home page contains links to some screen shots of the interactive GUI. The Web site contains some initial (rudimentary) documentation.

See the Reference Manual for more details on the segmenter. You can read about downloading and installing the program on your computer. The pre-alpha level source code is on the open2dprot.sourceforge.net CVS server. In addition, snapshots of the Java source code are available the SourceForge Files mirror server.

Examples - samples of screen shots

To give the flavor of running the segmenter, we provide a few screen shots of the graphical user interfaces and some images generated by the segmenter for the initial version of the segmenter. You can these images in the list below or view all of the screen shots in a single Web page.

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     Seg2Dgel is a contributed program available at Open2Dprot.sourceforge.net/Seg2Dgel
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         Revised: 01/25/2006