daime: Digital Image Analysis in Microbial Ecology
About daime
daime is a scientific image analysis and visualization software for microbiology, microbial ecology, and microbiome research.
It works with 2D and 3D microscopy datasets of microorganisms labeled by fluorescence in situ hybridization (FISH) or other fluorescence staining methods. daime analyzes cells and cell aggregates across various sample types including biofilms, flocs, animal and plant tissues, and microbial enrichment cultures and isolates.
daime is an acronym for "digital image analysis in microbial ecology".
Terms of Use
daime is free, open-source software published under the GNU General Public License (GPL).
Literature 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. Full text.
We kindly ask users to cite this paper if they have used daime in a published study.
Features
daime offers many features for image import, image processing and segmentation, image analysis, and visualization which are tailored to the needs of microbiome research. All functions are fully integrated and accessible through a user-friendly graphical interface. No programming skills are needed to use daime.
Widespread Use
daime has been used in hundreds of studies across microbial ecology, medical microbiology, microbiome research, and environmental engineering. Its 3D visualization capabilities were used to render the cover illustrations of "Brock - Biology of Microorganisms" (12th edition) and of PNAS vol. 103(7).
Download
daime is available for Microsoft Windows, Apple macOS, and Linux.
We provide ready-to-use binary packages. Users who prefer to compile daime themselves for a specific platform can download the source code along with instructions.
Sample images and a step-by-step tutorial are provided to help new users become acquainted with the features and workflows of the software.