Free and open source

NumPy (Numerical Python) is an open source Python library that’s used in almost every field of science and engineering. It’s the universal standard for working with numerical data in Python, and it’s at the core of the scientific Python and PyData ecosystems. The NumPy library contains multidimensional array and matrix data structures. It provides ndarray, a homogeneous n-dimensional array object, with methods to efficiently operate on it. NumPy can be used to perform a wide variety of mathematical operations on arrays.

NumPy users include everyone from beginning coders to experienced researchers doing state-of-the-art scientific and industrial research and development. The NumPy API is used extensively in Pandas, SciPy, Matplotlib, scikit-learn, scikit-image and most other data science and scientific Python packages. 

Learn more about NumPy here!

SciPy is a collection of mathematical algorithms and convenience functions built on the NumPy extension of Python. It adds significant power to the interactive Python session by providing the user with high-level commands and classes for manipulating and visualizing data. With SciPy, an interactive Python session becomes a data-processing and system-prototyping environment. Find more about SciPy here!

Neuroconductor is an open-source platform for rapid testing and dissemination of reproducible computational imaging software, specialized in brain medical imaging (MRI, fMRI, DTI, etc...) but that could be used on a wider range of images. The goals of the project are to:

• provide a centralized repository of R software dedicated to image analysis;
• disseminate quickly software updates;
• educate a large, diverse community of scientists using detailed tutorials and short courses;
• ensure quality via automatic and manual quality controls; and
• promote reproducibility of image data analysis.

Based on the programming language R, Neuroconductor starts with 68 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing.

CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in-silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D intuitive and make Virtual Tissue modeling accessible to users without extensive software development or programming experience.

It uses Cellular Potts Model to model cell behavior.

Elastix is a toolbox for rigid and nonrigid registration of (medical) images.

Elastix is based on the ITK library, and provides additional algorithms for image registration. 

The software can be run as a single-line command, making it easy to include in larger scripts or workflows. The user needs to edit a configuration file that contains all relevant parameters for registration: transformation model, metric used to comapre images, optimization algorithm, mutliscale pyramidal representation of images...

Nowadays elastix is accompanied by SimpleElastix, making it available in other languages like C++, Python, Java, R, Ruby, C# and Lua.