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Image Processing and Analysis


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.

Among the licensed software available there are 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).


Among the freeware software there is 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 analysisCell 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:


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).

plugins - Centromere Recognition and Quantification (analysis of Protein Turnover by Quantitative SNAP-Based Pulse-Chase Imaging).


Huygens -

Imaris -


Image J -

FiJi -

Cell Profiler and CP Analyst -

GNU Octave -

Cell File Analyzer –

MIQuant -

LCFs -


IN Cell Investigator -