CMEIAS-IT v.1.28 Image Analysis system requirements:
- Operating system: XP Pro or later, 32-bit or 64-bit
- Hard disk space needed: ~20 MB
- Essential -- UTHSCSA ImageTool Ver. 1.28 (installed with CMEIAS using the Setup.exe)
- Essential -- Software (e.g., Adobe Acrobat Reader DC) to view and print the pdf files of the CMEIAS 1.28 user manual and the CMEIAS Tutorial Worksheet
- Essential for installation -- A program to unzip downloaded setup file of the CMEIAS-IT v. 1.28 application in your computer
- Recommended -- Program applications typically used in conjunction with CMEIAS/ImageTool for image analysis include an image editing program (e.g.,CMEIAS Color Segmentation), a Windows-compatible spreadsheet program, and a statistics/graphics program
Essential steps required for accurate image analysis of microorganisms using CMEIAS:
CMEIAS-IT Ver. 1.28 image analysis software is now installed as a stand-alone program application.
- The first requirement for accurate image analysis is a high quality primary image acquired in photo, video, or digital format. For CMEIAS automated image analysis, the image must be converted to an 8-bit digital grayscale in an uncompressed file format [e.g., Tiff, BMP] that can be opened in CMEIAS-IT Ver. 1.28.
- For accurate morphotype classification, images must have adequate magnification and pixel resolution so that the smallest cell to be analyzed has sufficient pixel density (at least 30 pixels) to accurately define its morphotype and body size. This requirement poses no problem for skilled microscopists using research-quality optics and modern digital image acquisition and processing devices. Detailed instructions to adjust image size and resolution are provided in the CMEIAS user manual.
- ImageTool uses a brightness thresholding procedure to find the foreground objects of interest in 8-bit grayscale images. This requires that all pixels of foreground objects have brightness values that lie outside the range that defines the background. Therefore, prior to analysis, the image may require editing in order to be fully segmented, i.e., reduced to the objects of interest using the brightness thresholding procedure in ImageTool. All this image editing work must precede CMEIAS object analysis and morphotype classification. ImageTool features some image editing routines, but digital images of microbial communities will often require additional interactive editing tasks to achieve object segmentation, e.g., splitting of touching objects, removal of invalid objects or background pixels whose brightness values lie within the range that includes the objects of interest. A CMEIAS Color Segmentation application is available to facilitate object segmentation in color and grayscale images with complex backgrounds. Other image segmentation tools are under development and will be released in future CMEIAS upgrades.
See the Step-by-Step Demo for the procedures required to perform object analysis and morphotype classification of microbial communities.
Refer to the Liu et al. 2001 publication, the CMEIAS User Manual provided in the CMEIAS-IT Ver. 1.28 and the CMEIAS Color Segmentation downloads for detailed instructions to acquire and edit digital images, perform object analysis, and classify microbial morphotypes using CMEIAS/ImageTool.
CMEIAS Color Segmentation Ver. 1.0 system requirements:
- This program operates on a PC with a 32-bit or 64-bit operating system (Windows XP Pro or later) ideally with 1-GHz processor or higher and 1 GB RAM or higher
- Hard disk space needed: 26 MB
- A media player (e.g., VLC) to view the step-by-step audio-visual demo (CmeiasColorSegmentation.wmv)
- Refer to the Gross et al. 2009 publication and the CMEIAS Color Segmentation User Manual for detailed information on using this software to process images for object segmentation
CMEIAS Quadrat Maker Ver. 1.0 system requirements:
- Operating system: Windows XP Pro or later, 32-bit or 64-bit
- Hard disk space needed: 26 MB
- Software to unzip the CmeiasQuadratMaker.zip download file
- Software (e.g., Adobe Acrobat Reader DC) to view and print the CMEIAS Quadrat Maker User Manual (pdf)
- A media player (e.g., VLC) to view the step-by-step audio-visual demo (CmeiasQuadratMaker.wmv)
- Input images can be 8-bit grayscale or 24-bit RGB in tif, bmp, png, or jpg file format
CMEIAS JFrad Ver. 1.0 system requirements:
- Essential -- Java standard edition, recommend ver. 8 or higher, free and available at http://www.java.com/en/
- Operating system: 32- or 64-bit. All features are available to both Windows and non-Windows users
- Hard disk space needed: 32.5 MB
- Software to unzip the CmeiasJFrad.zip download file
- Software (e.g., Adobe Acrobat Reader DC) to view and print the CMEIAS JFrad User Manual (pdf) and our publication describing CMEIAS JFrad in Microbial Ecology
- A media player (e.g., VLC) to view the step-by-step audio-visual demo (CmeiasJFrad.wmv)
- Input images can be 8-bit grayscale or 24-bit RGB in tif, bmp, png, jpg or gif file format