scholarly journals OP5 - A 3D-Fourier-Descriptor Approach to Compress and Classify 3D Imaging Data

2009 ◽  
Author(s):  
Robert Schmitt ◽  
Peter Fritz
Keyword(s):  
3D Imaging ◽  
Fourier Descriptor ◽  
Imaging Data ◽  
Descriptor Approach

scholarly journals Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
David M Young ◽  
Siavash Fazel Darbandi ◽  
Grace Schwartz ◽  
Zachary Bonzell ◽  
Deniz Yuruk ◽  
...  
Keyword(s):  
Mouse Brain ◽  
3D Imaging ◽  
Developmental Stages ◽  
Brain Atlas ◽  
Imaging Data ◽  
Qualitative And Quantitative ◽  
Atlas Construction ◽  
Manual Curation ◽  
Developing Mouse Brain ◽  
2D Data

3D imaging data necessitate 3D reference atlases for accurate quantitative interpretation. Existing computational methods to generate 3D atlases from 2D-derived atlases result in extensive artifacts, while manual curation approaches are labor-intensive. We present a computational approach for 3D atlas construction that substantially reduces artifacts by identifying anatomical boundaries in the underlying imaging data and using these to guide 3D transformation. Anatomical boundaries also allow extension of atlases to complete edge regions. Applying these methods to the eight developmental stages in the Allen Developing Mouse Brain Atlas (ADMBA) led to more comprehensive and accurate atlases. We generated imaging data from 15 whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries). We provide the pipeline as the MagellanMapper software and the eight 3D reconstructed ADMBA atlases. These resources facilitate whole-organ quantitative analysis between samples and across development.

A Fourier Descriptor Approach to Integrated Type and Dimensional Synthesis of Coupled Serial Mechanism for Motion Generation

2019 ◽  
Author(s):  
Hao Lv ◽  
Yuanfei Han ◽  
Xiangyun Li ◽  
Liuxian Zhu
Keyword(s):  
Fourier Descriptor ◽  
Dimensional Synthesis ◽  
Type Synthesis ◽  
Motion Generation ◽  
End Effector ◽  
Novel Approach ◽  
Descriptor Approach ◽  
Harmonic Components ◽  
The Given ◽  
Serial Mechanism

Abstract Coupled serial mechanism is a class of mechanisms that couple the relative rotation of successive links utilizing gears or cable-pulley systems. They can be used to generate complex end-effector trajectories or motions with a single actuator. With the employment of Fourier descriptors, a novel approach to integrate type synthesis and dimensional synthesis of such mechanisms is proposed in this paper. Through the Fourier analysis of two arbitrary trajectories from the given motion, the simplest trajectory that contains the least number of harmonic components is identified. Then, characteristic information of those harmonics such as their numbers, amplitudes and initial phases are used to determine the topology and dimensions of the corresponding coupled serial mechanism, thus effectively solving the motion synthesis problem of this type of mechanisms. Finally, three examples are given to demonstrate the validity of the proposed method.

scholarly journals Constructing and Optimizing 3D Atlases From 2D Data With Application to the Developing Mouse Brain

2020 ◽  
Author(s):  
David M Young ◽  
Siavash Fazel Darbandi ◽  
Grace Schwartz ◽  
Zachary Bonzell ◽  
Deniz Yuruk ◽  
...  
Keyword(s):  
Mouse Brain ◽  
3D Imaging ◽  
Developmental Stages ◽  
Brain Atlas ◽  
Imaging Data ◽  
Qualitative And Quantitative ◽  
Atlas Construction ◽  
Manual Curation ◽  
Developing Mouse Brain ◽  
2D Data

Abstract3D imaging data necessitate 3D reference atlases for accurate quantitative interpretation. Existing computational methods to generate 3D atlases from 2D-derived atlases result in extensive artifacts, while manual curation approaches are labor-intensive. We present a computational approach for 3D atlas construction that substantially reduces artifacts by identifying anatomical boundaries in the underlying imaging data and using these to guide 3D transformation. Anatomical boundaries also allow extension of atlases to complete edge regions. Applying these methods to the eight developmental stages in the Allen Developing Mouse Brain Atlas (ADMBA) led to more comprehensive and accurate atlases. We generated imaging data from fifteen whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries). We provide the methods as the MagellanMapper software and the eight 3D reconstructed ADMBA atlases. These resources facilitate whole-organ quantitative analysis between samples and across development.

scholarly journals LAMA: automated image analysis for the developmental phenotyping of mouse embryos

Development ◽  
2021 ◽  
Vol 148 (18) ◽  
pp. dev192955
Author(s):  
Neil R. Horner ◽  
Shanmugasundaram Venkataraman ◽  
Chris Armit ◽  
Ramón Casero ◽  
James M. Brown ◽  
...  
Keyword(s):  
3D Imaging ◽  
Automated Image Analysis ◽  
Incomplete Penetrance ◽  
Imaging Data ◽  
Micro Computed Tomography ◽  
Sample Number ◽  
Automated Annotation ◽  
International Mouse Phenotyping Consortium ◽  
Automated Phenotyping ◽  
Wild Type Control

ABSTRACTAdvanced 3D imaging modalities, such as micro-computed tomography (micro-CT), have been incorporated into the high-throughput embryo pipeline of the International Mouse Phenotyping Consortium (IMPC). This project generates large volumes of raw data that cannot be immediately exploited without significant resources of personnel and expertise. Thus, rapid automated annotation is crucial to ensure that 3D imaging data can be integrated with other multi-dimensional phenotyping data. We present an automated computational mouse embryo phenotyping pipeline that harnesses the large amount of wild-type control data available in the IMPC embryo pipeline in order to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity. We also investigate the effect of developmental substage on automated phenotyping results. Designed primarily for developmental biologists, our software performs image pre-processing, registration, statistical analysis and segmentation of embryo images. We also present a novel anatomical E14.5 embryo atlas average and, using it with LAMA, show that we can uncover known and novel dysmorphology from two IMPC knockout lines.

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