Contents

Mean shift is a filter which acts as edge preserving filter similarly to non local mean or anisotropic diffusion. 

Mean shift can be used for denoising, segmentation or clustering. Two parameters are to be tuned, a spatial size of a patch and a gray level or color distance on which the algorithm is applied.

The phase contrast microscopy segmentation toolbox (PHANTAST) is a collection of open-source algorithms and tools for the processing of phase contrast microscopy (PCM) images. It was developed at University College London's department of Biochemical Engineering and CoMPLEX.

An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.

It implements the template matching function from the OpenCV library. The java interface of OpenCV was done through the javacv library.

This ImageJ plugin contains two functions. The first one is the cvMatch_Template. It implements the template matching function from the OpenCV library.

Deep learning based restoration, with guidelines for training. See also the Fiji plugin.

See more CSBDeep in Knime.

Deep learning for fluorescence image restoration (denoising, deconvolution). Requires training on your data set but the procedure is described.

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!

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.

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:

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.