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Name
Free-D
Byline
INRA, France
Description
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
Creator
Philippe Andrey
Contact
philippe.andrey@versailles.inra.fr
WWW
Free-D home page
Availability
Freely available
How to get
Download from the web site
Current version
1.09
Current version release date
2013.01.15
Open source
No
License
Custom
Available free of charge
Yes
Requirements
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.
Keywords
3D modeling, 3D reconstruction, atlas, microscopy, registration, segmentation, visualization
Platforms
Linux, MacOS, Windows
IATR listing last updated
26 Jan 2013