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It utilised image processing algorithms from the Functional Magnetic Resonance Imaging of the Brain (FMRIB) Software Library FSLL) [21], C3D [22], and NIFTIREG [23] software packages for image registration and re-sampling.
Several open-source packages for image analysis include functionality for machine learning-based cell classification.
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Overall processing and analysis was made by using HDF View, IDRISI macro-modeler to automate workflows for batch processing, ArcGIS spatial analysis toolbox and R raster package for image analysis.
ImageJ ([email protected]) was used as the software package for image processing.
SigmaScan is a flexible package for image analysis and SigmaScan Pro can be programmed with a specific macro language.
gitter is implemented in an open-source R package available from http://cran.r-project.org/web/packages/gitter and uses the EBImage (Pau et al. 2010) package for image manipulation and the ggplot2 (Wickham 2009) package for visualizations.
There have been a variety of software packages developed for image cytometry both on the commercial and academic sides [22]; however, there are no general purpose software packages designed to address particular situations.
Bsoft is a software package written for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing.
The EZ-C1 software package was used for acquisition and the NIS-Elements software package (Nikon Instruments Inc., Canada) for image processing.
Although figure of image quality and information capacity indexes were tested on a generic software package, their utilization for image quality characterization, in dedicated medical image software, will be useful provided there is image processing capability [ 59– 63].
The aXis2000 software package was used for image and spectra processing [72].
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