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JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

Ribes D, Parafita J, Charrier R, Magara F, Magistretti PJ, Thiran JP - PLoS ONE (2010)

Bottom Line: This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license.The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis.Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

View Article: PubMed Central - PubMed

Affiliation: Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

ABSTRACT
In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

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Intra-subject 3D reconstruction procedure.(A) Sections are first stacks in the Z direction. (B) Consecutive sections are extracted and down-sampled by a factor of four (for the first iteration, the two central sections are extracted). (C) Consecutive sections are co-registered and replace in the stacked volume. (D) The procedure ends when all sections have been aligned to the consecutive or the previous one.
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pone-0014094-g002: Intra-subject 3D reconstruction procedure.(A) Sections are first stacks in the Z direction. (B) Consecutive sections are extracted and down-sampled by a factor of four (for the first iteration, the two central sections are extracted). (C) Consecutive sections are co-registered and replace in the stacked volume. (D) The procedure ends when all sections have been aligned to the consecutive or the previous one.

Mentions: First, autoradiographic reconstructed volumes are obtained by stacking coronal sections in the z direction. Each section is then sequentially aligned to the adjacent one, starting with central sections [11]. The alignment is done using a rigid registration (6-degrees of freedom) based on minimizing normalized cross correlation cost function. To reduce registration computation time, each section is first down-sampled by a scaling factor of four (see figure 2A).


JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

Ribes D, Parafita J, Charrier R, Magara F, Magistretti PJ, Thiran JP - PLoS ONE (2010)

Intra-subject 3D reconstruction procedure.(A) Sections are first stacks in the Z direction. (B) Consecutive sections are extracted and down-sampled by a factor of four (for the first iteration, the two central sections are extracted). (C) Consecutive sections are co-registered and replace in the stacked volume. (D) The procedure ends when all sections have been aligned to the consecutive or the previous one.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2991313&req=5

pone-0014094-g002: Intra-subject 3D reconstruction procedure.(A) Sections are first stacks in the Z direction. (B) Consecutive sections are extracted and down-sampled by a factor of four (for the first iteration, the two central sections are extracted). (C) Consecutive sections are co-registered and replace in the stacked volume. (D) The procedure ends when all sections have been aligned to the consecutive or the previous one.
Mentions: First, autoradiographic reconstructed volumes are obtained by stacking coronal sections in the z direction. Each section is then sequentially aligned to the adjacent one, starting with central sections [11]. The alignment is done using a rigid registration (6-degrees of freedom) based on minimizing normalized cross correlation cost function. To reduce registration computation time, each section is first down-sampled by a scaling factor of four (see figure 2A).

Bottom Line: This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license.The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis.Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

View Article: PubMed Central - PubMed

Affiliation: Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

ABSTRACT
In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

Show MeSH