BIP: Biofilm Image Processing

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BIP: Biofilm Image Processing

        Overview
        Download
        Install
        Manual
                  Run the Program
                  Batch Image Processing
                  Single Image Processing

Overview

The natural mode of microbial growth is as organized biofilm communities on surfaces. It is now well established that it is very important to study bacteria such as Pseudomonas aeruginosa by growing it in the laboratory as a biofilm. The method is facilitated by the use of a confocal scanning laser microscopy (CSLM) that allows one to follow the development of the biofilm. The main difficulty faced is the quantitative and comparative analyses of the heterogeneous images. It was postulated that the bacterial biofilms have a fractal surface. An object is said to be fractal if its morphology does not change on different observation scales. If this conjecture is true then the mathematics of fractals imply that the two-dimensional cross-sections of the biofilms should have a fractal boundary. One way to establish fractal behavior is by studying the Fractal Dimension of the surface or that of the two-dimensional boundary along the cross section of the biofilm. In order to investigate the fractal behavior, we built a computer program called Biofilm Image Processing (BIP) to perform bulk processing of biofilm images produced by a CSLM. Since there is no consensus on a definition of the Fractal Dimension of a plane curve, our program computes it in eleven different ways. An analysis of the dependence of the fractal dimension on experimental parameters such as bacterial strains, nutrition concentration, and growth time was performed on a large number (over a thousand) of P. aeruginosa biofilm images. The merits and demerits of the different methods of computing the fractal dimension were studied.

There are no widely accepted definitions of FD. The software BIP computes it in 11 different ways. The methods include: Euclidean Distance Map (EDM), Minkowski Sausage Method (Dilation), Box Counting Method, Corner Method (Counting and Perimeter), Fast Method (Regular and Hybrid), Parallel Lines Method, Cumulative Intersection Method, and Mass Radius (Short and Long).

On the whole, biofilm images are about as fractal as can be expected within the variabilities in nature. The most stable and reliable methods are: EDM, Minkowski Sausage Method, and Box Counting Method.  Other interesting parameters like biomass & biovolume, surface area, distribution of thickness, behavior at substratum, roughness coefficient, diffusion parameters are underway.

VC++6.0 was used to develop this software.  It can perform bulk processing of biofilm images produced by a confocal scanning laser microscopy (SCLM).  A group of image processing tools such as histogram, threshold, delete noise, thin, smooth, expand, corner and so on were developed.
 
 
 

Download

Download is currently not available! Please e-mail: qichang_li@yahoo.com.

You can Free Download BIP demo version.  it will function only for half a year.  There are some limitations for the demo version.  You can only run 20 images per batch processing.  Serial Number Required for Installation is BIP-001

Download and installation steps
        1.On this page, click the Free Download button.
        2.In the Save As dialog box, choose the location to which you'd like to save the file.
        3.Click Save.
 

Install

Serial Number is required to install this software.

System requirement
    Platform:  Windows95, Windows98, WindowsNT

Installation steps
        1. Locate the file in its saved location and double-click it to unzip, save the files to a location you'd like to unzip to.
        2. Locate the file in the unziped location and double-click setup.exe to run setup.
        3. The BIP Setup window will recommend you exit all applications before continuing with the installation. Close all programs, then click Yes.
        4. The setup program will then present you with an End User License Agreement. Click Yes if you agree to comply.
        5. A dialog requesting the Serial Number will appear.  Input the Serial Number you required by clicking button
        6. Click OK.
        7. After you click OK, BIP Setup program will begin to install the software.

Trouble shoot
        If you can not install the software, make sure you used the right Serial Number (BIP-001).  Also, this program was only tested on Windows platform.
        If you can not run the software, make sure to adjust your computer time to the current time and install again.
        Further question, please e-mail to : qichang_li@yahoo.com, I am happy to answer any question related to this software.
 

Manual

Run the Program
    Click the Start menu, point to BIP, and then click BIP.  From the following dialog, you can select either BIP (single image processing) or PROJECT (batch image processing).





Batch Image Processing

If you selcet PROJECT, you will see the interface looks like the figure below.  If not, you may increase the resolution of you screen.


  1.   Select Images you want to process

    2. Use the standard windows file operation to locate the image files (there are some sample images installed in the same folder as this software).  Select a file in the Directory box, double clicking it or clicking Add will add this file to the Files in Project box.  You can add several files a time: Select the first file you want to add, when pressing Shift, click the last file you want to add, then all files between them will be selected,  then release Shift.  Also, by pressing Ctrl and clicking each file, you can select or de-select each file.  Then click Add button to add all the selected file into the Files in Project box.  By selecting files in the Files in Project box and clicking Delete button will delete the selected files from this box.
  1.   Addjust Parameters

    2. You can addjust parameters in the Image Parameters group.  For the sample images, just use the default values
  1.   Select Fractal Dimension Method

    2. From the Fractal Dimension Method box, select one of the eleven methods.
  1.   Calculate Fractal Dimension

    2. Click Calculate FD button, the software will process the images you select.  Through the scrolling of the selected highlight in the Files in Project box, you will see which image the software is processing.
  1.   View Fractal Dimension Result

    2. At the end of processing,  the result will be displayed in the three windows rightside.  The upper one displays the all fractal dimension of all images.  The lower two will display individual image and detail information of fractal dimension of that image.  You can select different file in the Files in Project box to view each individual result.





Single Image Processing

If you selcet BIP in the first dialog (clicking New button in the toolbox, or clicking File menu then New opens this dialog), you will see the interface looks like the figure below.  If not, you may increase the resolution of you screen.

    Open the image you want to process
    Click Load File... button, in the following standard open file dialog, select the image  (there are some sample images installed in the same folder as this software).


  1. Use Analysis Tools
  1. Click Histogram button displays the color distribution of the image in the right window


  1. Then click Threshold button display the threshold result by parameters


  1. Click Swap button, exchange the contents between the two windows


  1. Click Delete SP button deletes noises (small islands)


  1. Click Swap button


  1. Clicking Fill Holes button fills black areas in the island


  1. Click Swap button
    Clicking Get Edge button calculates the edges of islands


    Calculate Fractal Dimension
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  1. Addjust Parameters

    2. You can addjust parameters in the Image Parameters group.  For the sample images, just use the default values
  1. Select Fractal Dimension Method

    2. From the Fractal Dimension Method box, select one of the eleven methods.
    Animate the processing steps
    Check Animate below the Calculate FD button will animate the processing

    Click Calculate FD button, the software will process the image you select.


    View Fractal Dimension Result
    At the end of processing,  the result will be displayed in the three windows rightside.  The upper one displays the fractal dimension and the data used for Fit Regress.  The lower two will display the image and Fit Regress graphic.

Contact Person:

Dr. Giri Narasimhan
Associate Professor
School of Computer Science
Florida International University
Office: ECS 389
Phone: (305) 348-3748
Fax: (305) 348-3549
email: giri@cs.fiu.edu

Last modified on October 6th, 2000
Return to Dr. Giri Narasimhan