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INRA, France
A software for three-dimensional reconstruction and modelling of biological structures from stacks of serial sections (physical or virtual, as in confocal microscopy) and their quantitative analysis.

Original features include: (1) designed for the simultaneous processing and analysis of multiple stacks of possibly very large section images (up to several hundreds of megabytes per slice); (2) intuitive and efficient user interface: all the tools required for 3D reconstruction are integrated within a single application and communicate with each other, thus providing immediate feedback of any user action (segmentation, registration, etc.); (3) freely available for all major platforms (Linux, Windows and MacOSX).
NIfTI-1 support
Philippe Andrey
Free-D home page
Freely available
How to get
Download from the web site
Current version
Current version release date
Open source
Available free of charge
Technical publications
P Andrey & Y Maurin, 2005. Free-D: an integrated environment for three-dimensional reconstruction from serial sections. J. Neurosci. Methods, 145, 233-244.

E Maschino, Y Maurin & P Andrey, 2006. Joint registration and averaging of multiple 3D anatomical surface models. Comput. Vis. Image Understand., 101, 16-30.

The user manual (PDF) is available from the web site.
Applications publications
Banrezes B, Andrey P, Maschino E, Schirar A, Peytevin J, Rampin O, Maurin Y (2002). Spatial segregation within the sacral parasympathetic nucleus of neurons innervating the bladder or the penis of the rat as revealed by three-dimensional reconstruction. Neuroscience, 115, 97-109.

Burguet J, Andrey P, Rampin O, Maurin Y (2009). Three-dimensional statistical modeling of neuronal populations: illustration with spatial localization of supernumerary neurons in the locus coeruleus of quaking mutant mice. Journal of Comparative Neurology, 513, 483-495.

Schwartz J, Burguet J, Rampin O, Fromentin G, Andrey P, Tomé D, Maurin Y, Darcel N (2010). Three-dimensional macronutrient-associated Fos expression patterns in the mouse brainstem, PLoS ONE, 5, e8974.
Other information
Users can subscribe the Free-D mailing list to get informed of future releases, etc.
3D modeling, 3D reconstruction, atlas, microscopy, registration, segmentation, visualization
Linux, MacOS, Windows
IATR listing last updated
26 Jan 2013