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Dictyostelium discoideum
Microarray-SNAKES

Introduction
M-SNAKES is a robust, reliable and freely available software for spot finding and signal extraction from microarray images. Spot detection uses the model of a virtual, contractive and elastic closed chain. This method is based upon the active contour model (snakes; Koss et al. 1987, Int. J. Comput. Vision, 1, 321-331) and was recently used to detect cell edges in Dictyostelium discoideum (Dormann et al. 2002, Cell Motil. Cytoskeleton, 52, 221-230). The present approach has been implemented in Microsoft Visual Basic 6.0 (SP4).

Contact:
Thorsten Libotte
Institut für Biochemie Köln, Zentrum Biochemie
University of Cologne
http://home.vrweb.de/~libotte/


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Figure 1: M-SNAKES Interface.
Download of M-SNAKES (Zip file, 333 KB). The zip-file consists of additional OCX-files that have to be installed in the system-folder of your computer if they are not present (windows\system32).


M-SNAKES deals with 8 bit greyscale image data in BMP or JPEG format obtained by scanning of the microarray. To generate a stable, robust and user friendly software most of the parameters are fixed. Parameters that have to be adjusted individually are the image-force, the dimensions of the microarray and its sub-arrays and the mean distances between the spots.
Operating instruction
  1. Image Conversion
    Convert the microarray image (containing the original data) with an image processing software into a 8 bit greyscale image in BMP or JPEG format and save it.

  2. Run M-SNAKES
    To load the converted image, press the dummy button.

  3. Parameter
    Provide parameters for spot location
    • If a parameter file exists, load the parameter by pressing the dummy button
    • If the parameters are unknown enter the values manually
      • image force: to adjust the image-force short test runs can be run (see below). The greater the image-force the more the chain will be pushed away from regions of high contrast and vice versa. Typical values are between 0.1 and 0.9.
      • Parameters for main array: determine the distance (in pixels) between the spots of neighbouring subarrays with an image processing software. Write the calculated distances into the corresponding text fields of M-SNAKES. Enter the number of vertical (rows) and horizontal (columns) subarrays.
      • Parameters for subarray: determine the distance (in pixels) between the spots in a single subarray with an image processing software. Write the calculated distances into the corresponding text fields of M-SNAKES. Enter the number of rows and columns of spots per subarray.
      • To save the parameter, press the dummy button.

  4. Quantification
    To start the quantification the middle of the top left spot has to be marked with a mouse click and the dummy button has to be pressed. The image at half of the size with the detected spots marked by red circles will be automatically loaded into the interface of M-SNAKES.

  5. Saving results
    • To save the results, press the dummy button. By default M-SNAKES saves the files as "array.bmp" (image with the detected spots marked by red circles), and "array.txt" (intensitiy values). However, individual file names can be assigned.
    • The program offers the possibility to save the luminance values in the known GAL (Gene Pix Array List) format. For this option a GAL file has to be provided.


September 12, 2013
Institute of Biochemistry I, Cologne
Suggestions and wishes: Gudrun Konertz
Voice: +49 221 4786930
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