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The acquired images and image series were processed and analyzed with Fiji (image processing package, distribution of ImageJ).
The sidescan-sonar image processing package is part of the USGS Mini Image Processing System (MIPS) and has been designed to process data collected by any 'generic' digital sidescan-sonar imaging system.
Marabini, R. et al. Xmipp: An image processing package for electron microscopy.
The method was implemented as a plugin for the scientific open source image processing package ImageJ.
Sorzano, C.O. et al. XMIPP: a new generation of an open-source image processing package for electron microscopy.
Sorzano, C. O. et al. XMIPP: a new generation of an open-source image processing package for electron microscopy.
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For molecular imaging, several image processing packages "inherited" from EM can be used to average and analyze images of molecules; when the molecules are ordered in 2D crystals, lattice oriented algorithms can be used, while when the molecules are randomly arranged, single particle averaging approaches can be used.
Standard image processing packages (e.g. ImageJ) do not include this deconvolution option yet.
Image processing packages offer a solution because biodiversity monitoring and assessment using the conventional field techniques are time consuming and require large funds.
Though we provide implementations with graphical user interfaces in MATLAB, ImageJ and as a standalone tool, the open-source license used is permissive and allows for integration in other image processing packages as well as commercial solutions.
The commercial clinical PET scanners have high spatial resolution (~3 mm) and high sensitivity, and have streamlined and user-friendly image processing packages, including automated spatially explicit measurement of radiation attenuation by the plant tissues and soil [ 21].
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