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volker's picture


The jicbioimage [1] Python package makes it easy to explore microscopy data in a programmatic fashion. Exploring images via coding means that the exploratory work becomes recorded and reproducible. Furthermore, it makes it easier to convert the exploratory work into (semi) automated analysis work flows.

Features Built in functionality for working with microscopy data Automatic generation of audit trails IPython integration Cross-platform: Linux, Mac and Windows are all supported Works with Python 2.7, 3.3 and 3.4

Niko Kladt's picture


Image processing library for Python

scikit-image is a collection of algorithms for image processing. It is available free of charge and free of restriction. We pride ourselves on high-quality, peer-reviewed code, written by an active community of volunteers.

Niko Kladt's picture


OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). Python and Java bindings are also available. The Python binding includes a Deep Zoom generator and a simple web-based viewer. The Java binding includes a simple image viewer.

kota's picture


v3dlib library is a cross-platform C++ library written in wxWidgets for displaying 3D images. The most important part of the library is a window that can display 3D images of various types (RGB, RGB16, GRAY8, GRAY16, and float). The window can easily be extended of a new functionality and is used in many applications (e.g., viewer3d, Acquiarium, batchcrop, and others).

kota's picture


OpenCV is released under a BSD license and hence it’s free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 6 million.

kota's picture


Python(x,y) is a free scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment.

Many python libraries related to numerical calculation are packaged, so you do not need to search and install them individually.

Included libraries are listed here.

dscho's picture


BioImage Analysis Tool for all! See [1].

ImageJ 1.x


dscho's picture


ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data. It is widely used and contributed in the medical imaging field.


dscho's picture


EBImage is an open source image processing and analysis package for the statistical programming language R. Its primary goal is to enable automated analysis of large sets of images such as those obtained in high-throughput screening. An extensive range of basic image processing and feature extraction methods are provided. EBImage is available through the Bioconductor software project (



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