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

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!

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.

NiftyNet is a TensorFlow-based open-source convolutional neural networks (CNNs) platform for research in medical image analysis and image-guided therapy. NiftyNet’s modular structure is designed for sharing networks and pre-trained models. Using this modular structure you can:

• Get started with established pre-trained networks using built-in tools;
• Adapt existing networks to your imaging data;
• Quickly build new solutions to your own image analysis problems.