BioImage Information Index

Biii is a website for organizing bioimage analysis resources. We manually edit following pages, for you to search tools, workflows and functions for bioimage analysis:

Please enjoy!

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kota's picture

3D Slicer

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 Mac Os X.

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ASAP is an open source platform for visualizing, annotating and automatically analyzing whole-slide histopathology images. It consists of several key-components (slide input/output, image processing, viewer) which can be used seperately. It is built on top of several well-developed open source packages like OpenSlide, Qt and OpenCV but also tries to extend them in several meaningful ways.

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MyTardis is free and open-source data management software. It facilitates annotation, sharing and archiving of data and metadata collected from different modalities. It focuses on integration with scientific instruments, instrument facilities and research storage and computing infrastructure; to address the challenges of data storage, data access, collaboration and data publication.

maree's picture


QuPath is open source software for Quantitative Pathology. QuPath has been developed as a research tool at Queen's University Belfast.

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Neurolucida is a powerful tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis of neurons, such as quantifying 1) the number of dendrites, axons, nodes, synapses, and spines, 2) the length, width, and volume of dendrites and axons, 3) the area and volume of the soma, and 4) the complexity and extension of neurons.
See [1]


irene's picture

BSIF (Binarized Statistical Image Features)

Matlab Image Processing Toolbox
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Pyxit Landmark detection