Bioimage informatics

Please also check out ImageJ and Fiji.

This script includes a rough feature detection and then fine 2D Gaussian algorithm to fit Gaussians within detected regions. This macro is unique because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around this by linearising the equation. This implementation is for isotropic (spherical) or anistropic (longer in x/y) diagonally covariant Gaussians but not fully covariant Gaussians (anisotropic and rotated). 

The Cython language is a superset of the Python language that additionally supports calling C functions and declaring C types on variables and class attributes. This allows the compiler to generate very efficient C code from Cython code. This makes Cython the ideal language for wrapping external C libraries, embedding CPython into existing applications, and for fast C modules that speed up the execution of Python code.

SimpleITK provides a simplified interface to ITK in a variety of languages. A user can either download pre-built binaries, if they are available for the desired platform and language, or SimpleITK can be built from the source code. Currently, Python binaries are available on Microsoft Windows, GNU Linux and Mac OS X. C# and Java binaries are available for Windows. We are also working towards supporting R packaging.

R wrapper around the OMERO Java Gateway, to enable access to OMERO via R using rJava