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!

kozubek's picture

Clustered cell nuclei

Biological object: 
in silico clustered cell nuclei
Size (MB): 
11 200
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).

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Vaa3D [1, 2, 3] is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions ... It is also Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily...

irene's picture


QuantCenter is the framework for 3DHISTECH image analysis applications. with the goal of helping the pathologists to diagnose in an easier way.

QuantCenter, is optimized for whole slide quantification. It has a linkable algorithm concept that tries to provide an easy-to-use and logical workflow. The user has different quantification modules that he or she could link one after other to fine-tune or to speed up the analysis.

kota's picture


μManager is a software package for control of automated microscopes.

maree's picture


Cytomine is a rich internet application using modern web and distributed technologies (Grails, HTML/CSS/Javascript, RESTful API, Docker), databases (spatial SQL and NoSQL), and machine learning (it currently includes tree-based approaches with random subwindows) to foster active and distributed collaboration and ease large-scale image exploitation.

Ofra Golani's picture

Image Analysis Course for Life Science by Morten Larsen, University of Copenhagen

Image Analysis Course for Life Science Faculty.
Material includes: slides, hands-on exercises using ImageJ and related data.
There is a full lecture on ImageJ macro language (session 12).
Website: []

Session 1: The basics: Images - Digital image representation, Image processing and image analysis, Concerns at image acquisition, Pixel-wise transformations, Visual enhancement

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OpenMOLE (Open MOdeL Experiment) is a workflow engine designed to leverage the computing power of distributed execution environments for naturally parallel processes. A process is told naturally parallel if the same computation runs many times for a set of different inputs, such as model experiment or data processing… It is free software distributed under the AGPLv3 free software license.

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