daime is a digital image analysis and 3D visualization program trimmed to the needs of biologists who explore microorganisms in situ in environmental and medical samples. daime offers special tools for analyzing microbial cells that were stained by fluorescence labelling techniques (such as FISH with rRNA-targeted probes).
 
A feature on daime has recently appeared in the Research Highlight section of Nature Reviews Microbiology (2006; 4: 167).

The cover illustrations of "Brock - Biology of Microorganisms" (12th edition) and of PNAS vol. 103(7) were rendered by daime.

 
Features of daime include:

  • Batch import and analysis of large image series and confocal z-stacks
  • Analysis and visualization of colour or grayscale images
  • Methods for noise reduction, background removal, and other image editing functions
  • Automated 2D and 3D image segmentation based on various thresholding and edge detection algorithms
  • Colour-based image segmentation
  • Quantitative analysis of spatial localization patterns (e.g. in biofilms): Do different microbial populations co-aggregate or do they avoid each other?
  • Measurement of cells and cell aggregates (size, brightness, many other features) in 2D and 3D
  • Quantification of the in situ abundance of microorganisms
  • Evaluation of rRNA-targeted oligonucleotide probes used in fluorescence in situ hybridization (FISH): Which hybridization stringency is needed for optimal probe specificity?
  • 3D visualization of confocal image stacks by fast volume rendering. Rotation, "fly-through", colorization, semi-transparent rendering, shadows, and clipping at interactive speed on commodity PCs
  • Definition of complex 3D animations via a simple user interface
Please click  here for a more detailed description of selected features.
 
System requirements and installation
daime is available for Linux and for Microsoft Windows (2000, XP, Vista, and 7). Please refer to the  installation manual for a detailed list of hardware and software requirements and for installation instructions.
 
Availability and price of daime
daime is published under the GNU Public License (GPL) and is free of charge. However, we ask all users to cite the original daime paper if their own published results were obtained by using daime.
Please visit the  download section for further information.
 
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Reference
Daims H, Lücker S, Wagner M. 2006. daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol. 8: 200-213.
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daime is developed by  Holger Daims.
Questions, bug reports and comments can be sent to: