Comstat User Manual
COMSTAT is a program for quantification of three-dimensional biofilm structures. It analyzes stacks of images acquired with confocal laser scanning microscopy (SCLM). It was written as a script in MATLAB 5.3 (The MathWorks Inc., Natick, Massachusetts), equipped with the Image Processing Toolbox. The program is menu controlled, user-friendly, and requires no prior knowledge in programming or image analysis. MATLAB 5.3 equipped with the Image Processing Toolbox must be available on your computer. Later versions of MATLAB will also work fine.
Image formats
COMSTAT analyzes image stacks acquired with SCLM. Unfortunately, different confocal microscopes (Leica, Zeiss, Olympus, Nikon, Biorad) usually store image data in different formats. COMSTAT was originally designed to analyze images from the Leica TCS4D confocal microscope. However, COMSTAT can also analyze images in other formats, which will be described below.
At present, COMSTAT requires all images of a stack to be stored as individual ‘.tif’ images. The ‘.tif’ images can be of any sizes (e.g. 256×256, 512×512 and 1024×1024), and be 8-bit, 16-bit or 32 bit. However, all of the programs will convert the images into grey-scale 8-bit images. Using 8-bit 512×512 images is fine for the purpose of quantifying biofilm structures. COMSTAT requires an ‘.info’ file for each stack of images. An ‘.info’ file is a text file containing information about the image stack. COMSTAT uses informations from the ‘.info’ file when analysing the image stack, and it is therefore essential that the ‘.info’ file is present. The Leica TCS4D microscope automatically generates an ‘.info’ file when an image stack is saved. The Leica TCS4D ‘.info’ file contains image information such as the time and date of acquisition, pinhole size, pixel sizes, etc. COMSTAT reads informations about the image stack from the ‘.info’ file. However, if you do not have a Leica TCS4D microscope you can still write your own ‘.info’ files, which can be read by COMSTAT.
Get pdf Comstat User Manual
