3D segmentation (reconstruction) and modeling using Free-D

Free-D (http://free-d.versailles.inra.fr/) is a 3D reconstruction and modeling software. It is multiplatform, free (but not open source) tool for academic research and teaching.

Here is how to proceed, using Free-D:

1. Segmentation:

* load (a collection of) individual 3d stacks

* (optional for serial sections) perform a 2D registration to align image slices

* segment/reconstruct 3D contours using snakes

* segment 3D spots

2. Construct average cell:

* normalize the contours to compute a average cell, by registering/warping 3D contours/surfaces

3. Quantification:

* project each individual cell to the average one

* build density maps to analyze (cartography)

A few notes for current software version (till 10/2016):

* input file format: tiff (not able to import bioformats)

* currently results are saved in customized format, but there is an exportor to convert this format into fiji readable one

* import already generated contours is on the software's TODO list