After acquiring a microscopic image, the resulting digital image is generally processed.
The final outcome of the processing procedure can be either an improve image, or a set of parameters obtained from careful analysis and treatment of the image.
The PPBI consortium has several image analysis & processing software either licensed or freeware that will help the analysis of the obtained data, as well as greatly enhance the final image.
Licensed software available:
- Huygens (image restoration, visualization, and analysis);
- Imaris (data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets);
- MatLab (analyze data, develop algorithms, create models and applications);
- IN Cell Investigator (flexible and comprehensive solution for automated high-content analysis of live and fixed assays).
Freeware software available:
- Image J (display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images);
- Fiji (an image processing package. It can be described as a "batteries-included" distribution of ImageJ);
- Cell Profiler (open-source platform for automated image analysis);
- Cell Profiler Analyst (open-source software for exploring and analyzing large, high-dimensional image-derived data);
- GNU Octave(high-level language, primarily intended for numerical computation).
PPBI also as available “in house” developed software and plugins for ImageJ/Fiji:
- Plugins
Centromere Recognition and Quantification (analysis of Protein Turnover by Quantitative SNAP-Based Pulse-Chase Imaging).
- Software
MIQuant (automatization the infarct extension estimation in animal models);
Cell File Analyzer (detection of cell files - the main structure in plant roots);
LCFs (detection of cell nuclei and joint detection of cytoplasm without the use of image segmentation).
- Repository
Search Engine for BioImage Analysis (SE4BIA).
