SYNOPSIS

Free-D is a three-dimensional (3D) reconstruction and modeling software. It allows to generate, process and analyze 3D point and surface models from stacks of 2D images.

Free-D is an integrated software, offering in a single graphical user interface all the functionalities required for 3D modeling. It runs on Linux, Windows, and MacOS.

Free-D is developed by the Modeling and Digital Imaging team of the Institut Jean-Pierre Bourgin, INRA Versailles, France.

LATEST RELEASE: Free-D 1.15 (2018.10.29). See the major changes here.

FEATURES

		Stack browsing > can handle multiple stacks of several hundreds of Gb > can handle section images of several hundreds of Mb > supports variable inter-slice spacing and pixel calibration
		Image segmentation > manual delineation and pointing on 2D images > automated 2D and 3D segmentation (contours, spots) > segmentation editing, resampling, and smoothing
		Image registration > interactive rigid transformations (translation and rotation) > several display modes for registration visualization > registration based on images and/or segmentations
		Model reconstruction > instant rendering of segmentation and registration actions > easy navigation through series of stack reconstructions > permanent storage of poses of interest
		Quantitative analysis > quantitative measures (counts, lengths, areas, volumes, etc.) > analysis per slice, per 2D item, per 3D reconstructed model > export as spreadsheet for further statistical analysis
		Spatial normalization and atlasing > groupwise 3D shape registration and averaging > linear and non-linear spatial normalization > statistical density estimation and visualization

DOWNLOAD

Conditions of use

Free-D is freely available for academic research or teaching purposes. Please contact us for any other usage. Free-D is distributed as is, without any warranty of any kind.

Users are asked to subscribe to the diffusion list before downloading and using Free-D.

Citation

Any publication of results generated using Free-D must include the following reference:

Andrey P & Maurin Y (2005). Free-D: an integrated environment for three-dimensional reconstruction from serial sections. Journal of Neuroscience Methods, 145, 233-244.

Any publication of results generated using the spatial normalization and density mapping module must include the following reference:

Biot E, Crowell E, Burguet J, Höfte H, Vernhettes S, Andrey P (2016). Strategy and software for the statistical spatial analysis of 3D intracellular distribution. Plant Journal, 87, 230-242.

The reference to the original algorithm for global shape registration and averaging available in the spatial normalization module is the following:

Maschino E, Maurin Y, Andrey P (2006). Joint registration and averaging of multiple 3D anatomical surface models. Computer Vision and Image Understanding, 101, 16-30.

The reference to the original polynomial warping algorithm available in the spatial normalization module is the following:

Andrey P, Maschino E, Maurin Y (2008). Spatial normalisation of three-dimensional neuroanatomical models using shape registration, averaging, and warping. Fifth IEEE International Symposium on Biomedical Imaging (ISBI'08): From Nano to Macro, pp. 1183-1186.

The reference to the original method for statistical parametric density mapping available in the spatial normalization module is the following:

Burguet J, Maurin Y, Andrey P (2011). A method for modeling and visualizing the three-dimensional organization of neuron populations from replicated data: properties, implementation and illustration. Pattern Recognition Letters, 32, 1894-1901.

Downloads

HELP

Manual

Download here the Free-D software manual (version 1.15, PDF). Contains a one-page quick start guide, a user manual, and a reference manual.

Diffusion list

The diffusion list is another source of information and documentation, in particular to get informed of future releases. Click here to subscribe to the diffusion list

Contact

Philippe ANDREY (philippe andrey AT inra fr).

PLUG-INS

MorphoLeaf

A plug-in for the quantitative multi-scale analysis of leaf (and others) morphodynamics.

More information and download on MorphoLeaf web page.

TOOLS

Below is a collection of tools related to Free-D (version 1.11-15). Conditions of use and citation as above.

sdfcheck

Checks and reports errors in .sdf files. This tool is in particular useful for debugging .sdf files edited/written by hand or generated by external applications.

Download sdfcheck for Linux 64 bits
Download sdfcheck for Windows 32 bits
Download sdfcheck for MacOS X

sdfexport

Exports selected or all reconstructed models from a .sdf file. Exported shapes can subsequently be loaded and visualized using sviewer without having to load images.

Download sdfexport for Linux 64 bits
Download sdfexport for Windows 32 bits
Download sdfexport for MacOS X

sviewer

The standalone version of Free-D's 3D rendering module. Loads and displays 3D shape files (using in-house file format). See sdfexport for generating such files from .sdf files.

Download sviewer for Linux 64 bits
Download sviewer for Windows 64 bits
Download sviewer for MacOS X

shapepca

Principal component analysis of registered shapes. Typically intended to run on 3D shapes previously registered using the spatial normalization module of Free-D.

Download shapepca for Linux 64 bits