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Free-D specifications


Unique identifier OMICS_10251
Name Free-D
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 1.11
Stability Stable
Maintained Yes


No version available


  • person_outline Philippe Andrey

Publication for Free-D

Free-D citations


Statistical Comparison of Spatial Point Patterns in Biological Imaging

PLoS One
PMCID: 3914854
PMID: 24505311
DOI: 10.1371/journal.pone.0087759

[…] l sections (30 thick) at the level of the SPN and the sections were digitized under light microscopy. Labeled neurons were manually segmented and 3D models of neuronal populations were computed using Free-D software . All experimental procedures are detailed in . By superimposing spatially normalized positions of BLD and CCV neurons ( animals per group), a segregation of the two populations along […]


Statistical Analysis of 3D Images Detects Regular Spatial Distributions of Centromeres and Chromocenters in Animal and Plant Nuclei

PLoS Comput Biol
PMCID: 2900307
PMID: 20628576
DOI: 10.1371/journal.pcbi.1000853

[…] rm on the distance map, and the nuclei from the cell types of interest were manually selected.Confocal image stacks of A. thaliana nuclei were processed and analyzed with programs developed using the Free-D software libraries . Each image stack contained a single nucleus. Images were automatically cropped to limit processing to a bounding box surrounding the nucleus. To separate the nucleus from t […]


Three Dimensional Macronutrient Associated Fos Expression Patterns in the Mouse Brainstem

PLoS One
PMCID: 2813867
PMID: 20126542
DOI: 10.1371/journal.pone.0008974

[…] rainstem (from Bregma −8.3 mm to Bregma −6.2 mm according to a stereotaxic atlas ) was sampled in coronal sections. Three-dimensional models of the brainstem and cell populations were generated using Free-D, a reconstruction and modeling software (). For this purpose, in each mouse, structures of interest identified on the digitized images were manually segmented: the brainstem contour and Fos po […]


3D fluorescent in situ hybridization using Arabidopsis leaf cryosections and isolated nuclei

Plant Methods
PMCID: 2731090
PMID: 19650905
DOI: 10.1186/1746-4811-5-11

[…] Confocal image stacks were automatically converted to a format enabling their processing by programs developed using the Free-D software libraries []. To separate the nucleus from the background, a preliminary intensity threshold was computed using the isodata algorithm []. Since this algorithm is sensitive to the relat […]


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Free-D institution(s)
Analyse et Modélisation en Imagerie Biologique, Neurobiologie de l’Olfaction et de la Prise Alimentaire, Institut National de la Recherche Agronomique, Domaine de Vilvert, Jouy en Josas, France

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