PMID- 16423009
OWN - NLM
STAT- MEDLINE
DCOM- 20060310
LR  - 20061115
IS  - 1462-2912 (Print)
IS  - 1462-2912 (Linking)
VI  - 8
IP  - 2
DP  - 2006 Feb
TI  - daime, a novel image analysis program for microbial ecology and biofilm research.
PG  - 200-13
AB  - Combinations of microscopy and molecular techniques to detect, identify and 
      characterize microorganisms in environmental and medical samples are widely used 
      in microbial ecology and biofilm research. The scope of these methods, which 
      include fluorescence in situ hybridization (FISH) with rRNA-targeted probes, is 
      extended by digital image analysis routines that extract from micrographs 
      important quantitative data. Here we introduce daime (digital image analysis in 
      microbial ecology), a new computer program integrating 2-D and 3-D image analysis 
      and visualization functionality, which has previously not been available in a 
      single open-source software package. For example, daime automatically finds 2-D 
      and 3-D objects in images and confocal image stacks, and offers special functions 
      for quantifying microbial populations and evaluating new FISH probes. A novel 
      feature is the quantification of spatial localization patterns of microorganisms 
      in complex samples like biofilms. In combination with '3D-FISH', which preserves 
      the 3-D structure of samples, this stereological technique was applied in a proof 
      of principle experiment on activated sludge and provided quantitative evidence 
      that functionally linked ammonia and nitrite oxidizers cluster together in their 
      habitat. This image analysis method complements recent molecular techniques for 
      analysing structure-function relationships in microbial communities and will help 
      to characterize symbiotic interactions among microorganisms.
FAU - Daims, Holger
AU  - Daims H
AD  - Department fur Mikrobielle Okologie, Universitat Wien, Vienna, Austria. 
      daims@microbial-ecology.net
FAU - Lucker, Sebastian
AU  - Lucker S
FAU - Wagner, Michael
AU  - Wagner M
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Environ Microbiol
JT  - Environmental microbiology
JID - 100883692
RN  - 0 (RNA Probes)
RN  - 0 (RNA, Bacterial)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - 0 (Sewage)
SB  - IM
MH  - Biofilms/*growth & development
MH  - Imaging, Three-Dimensional/*methods
MH  - In Situ Hybridization, Fluorescence
MH  - RNA Probes
MH  - RNA, Bacterial/analysis
MH  - RNA, Ribosomal, 16S/analysis
MH  - Sewage/*microbiology
MH  - *Software
EDAT- 2006/01/21 09:00
MHDA- 2006/03/11 09:00
CRDT- 2006/01/21 09:00
PHST- 2006/01/21 09:00 [pubmed]
PHST- 2006/03/11 09:00 [medline]
PHST- 2006/01/21 09:00 [entrez]
AID - EMI880 [pii]
AID - 10.1111/j.1462-2920.2005.00880.x [doi]
PST - ppublish
SO  - Environ Microbiol. 2006 Feb;8(2):200-13. doi: 10.1111/j.1462-2920.2005.00880.x.