daime is a novel computer program that integrates digital image analysis and 3-D visualization functions trimmed to the needs of microbiologists who want to explore the diversity, spatial localization, and ecophysiology of microorganisms in environmental and medical samples. It analyzes digital images acquired by epifluorescence and confocal laser scanning microscopy. We have developed daime and use it for our ongoing research projects. We make this program available to other scientists, who may find it useful for their own research in microbial ecology and other disciplines.
 
A feature on daime has recently appeared in the Research Highlight section of Nature Reviews Microbiology (2006; 4: 167).
 
Features of daime include:
  • Analysis of single images, image series and 3-D confocal image stacks
  • Automated and manual 2-D and 3-D image segmentation
  • Quantitative analysis of spatial localization patterns (e.g. in biofilms): Are different microbial populations colocalized in their habitats or do they avoid each other?
  • Measurement of brightness and size parameters of fluorescently stained cells
  • Basic functionality for object classification
  • Evaluation of rRNA-targeted oligonucleotide probes used in fluorescence in situ hybridization (FISH): Which hybridization stringency is needed for optimal probe specificity?
  • Quantification of the in situ abundance of microbial populations
  • Interactive 3-D visualization of confocal image stacks by high-speed volume rendering
  • Integration of image processing, image analysis and visualization in one software package, where all functions are linked to each other and are accessible via a convenient graphical user interface
Please click  here for a more detailed description of selected features.
 
System requirements
daime was originally developed on Linux, but the program is available for both Linux and Windows 2000/XP. Users who do not want to install Linux on their PCs in order to run daime can use a special daime CD, which will contain a full Linux operating system and (of course) daime. This bootable CD (to be available shortly) can be used on most PCs without any modifications of already installed operating systems.
 
Availability and price of daime
daime is published under GNU licenses and thus it is free of charge. However, we ask all users to cite us in their publications if their own published results were (directly or indirectly) obtained by using daime.
Please visit the  download section for further information.
 
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Reference
Daims H, Lücker S, Wagner M. 2005. daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol. 8: 200-213.
 PDF
 
daime has been developed by  Holger Daims.
Questions, bug reports and comments can be sent to: