Imaging Libraries

If you like this repository, please click on Star! If you use this package for your research, please cite our paper: BibTeX entry: This project is supported by the following institutions:

If you use DLTK in your work please refer to this citation for the current version: Setup a virtual environment and activate it. Although DLTK<=0.2.1 supports and python 2.7, we will not support i…

BibTeX entry: Copyright 2018 the NiftyNet Consortium.

The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. Segmentation is the process of identifying and class…

Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and …

Nilearn enables approachable and versatile analyses of brain volumes. It provides statistical and machine-learning tools, with instructive documentation & friendly community. Execute the followin…

This is an open-source python package for the extraction of Radiomics features from medical imaging. With this package we aim to establish a reference standard for Radiomic Analysis, and provide a te…

MedicalTorch is an open-source framework for PyTorch, implementing an extensive set of loaders, pre-processors and datasets for medical imaging.

The Common Toolkit (CTK) is a community-driven effort, focused on providing support code for medical image analysis, surgical navigation, and related projects. To work with CTK, you need to have a C+…

You can find our sources and single-click downloads: DIPY can be installed using pip: or using conda:

To install the latest development version, run: When working on NiBabel itself, it may be useful to install in "editable" mode:

ITKWidgets is an elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry. To install for all environme…

MedPy is an image processing library and collection of scripts targeted towards medical (i.e. high dimensional) image processing.

Tifffile is a Python library to Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, DNG, STK, LSM, SGI, NIHImage, ImageJ, MMStack, NDTiff, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, …

FAST is an open-source framework with the main goal of making it easier to do high-performance processing, neural network inference, and visualization of medical images utilizing multi-core CPUs and …

Installing ODL should be as easy as or ODL is compatible with Python 2/3 and all major platforms (GNU/Linux / Mac / Windows). This is an incomplete list of articles and projects using ODL. If you wan…

Finally the saved models are used for making predictions.Confusion Matrix is used as the Performance Metrics for this classifcation task.

A neural networks toolbox with a focus on medical image analysis in tensorflow/keras for now. If you use this code, please cite: If you are using any of the sparse/imputation functions, please cite:

Tools for tissue image stain normalization and augmentation in Python 3. Original images: Stain normalized images:

starfish supports python 3.7 and above and can easily be installed from PyPI: starfish will be dropping support for python 3.6 in the next release due to minimum python=3.7 version requirements in up…

Deep Reinforcement Learning (DRL) agents applied to medical images tensorpack-medical requires: New contributors of any experience level are very welcomed You can clone the latest version of the sour…

A Python library for coordinate- and image-based meta-analysis. Currently, NiMARE implements a range of image- and coordinate-based meta-analytic algorithms, as well as several methods for advanced m…

Whole-brain cell detection, registration and analysis. Basic usage: cellfinder takes a stitched, but otherwise raw whole-brain dataset with at least two channels: Classical image analysis (e.g. filte…

In the era of Deep Learning, developing robust machine learning solutions to problems in biomedical imaging requires access to large amounts of annotated training data, objective comparisons of state…

This Repo contains the Preprocessing Code for 3D Medical Imaging From the last year of my undergrad studies I was very queries about Biomedical Imaging. But until the starting my master I don't have …

Method 1 (stable) Method 2 (bleeding edge) Method 3 (for development)

Rejoice OpenCV users, a lightweight neuroimaging .nii to .png converter that actually works. Now supports both Python3 and Matlab 2017b! For those without Python, Pip or the modules, simply open Term…