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

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Chong Zhang

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Free-D ( 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

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