multi-channel

QuPath is open source software for Quantitative Pathology. QuPath has been developed as a research tool at Queen's University Belfast.

Neurolucida is a powerful tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis of neurons, such as quantifying 1) the number of dendrites, axons, nodes, synapses, and spines, 2) the length, width, and volume of dendrites and axons, 3) the area and volume of the soma, and 4) the complexity and extension of neurons. See 10.3389/fnins.2012.00049

SIMcheck is an ImageJ plugin suite for assessing the quality and reliability of Structured Illumination Microscopy (SIM) data. The quality of the raw data, the quality of the reconstruction and the calibration of the microscope can be tested. 

Nuget package for conversion between color spaces and calculation of color differences. Color spaces available: -CMY -CMYK -HSL -HSB -HSV -CIE L*a*b* -Hunter LAB -L*C*h* -L*u*v* -RGB -XYZ -YXY Color differences available: -CIE76 -CMC l:c -CIE94 -CIE2000. Online example at http://colormine.org/color-converter

Automatic registration in 2D or 3D based on detection or binary mask. Takes images with detections already done on it.