3D Brain Atlas Reconstructor Service—Online Repository of Three-Dimensional Models of Brain Structures

Majka, Piotr; Kowalski, Jakub; Natalia, Chlodzinska; Wójcik, Daniel K.

doi:10.1007/s12021-013-9199-9

Cited by 15 publications

(14 citation statements)

References 32 publications

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“…The workflow used there addresses a typical reconstruction task in which a 3D brain image is reconstructed from a series of stained sections and a reference image. Additionally, during its development, the framework was used to create stereotaxic atlas of the Monodelphis opossum brain (Majka et al 2013 ) and to construct a workflow for connectivity data mapping in the common marmoset brain (Majka et al 2014 ).…”

Section: Discussion and Summarymentioning

confidence: 99%

Possum—A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections

Majka

Wójcik

2015

Neuroinform

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Techniques based on imaging serial sections of brain tissue provide insight into brain structure and function. However, to compare or combine them with results from three dimensional imaging methods, reconstruction into a volumetric form is required. Currently, there are no tools for performing such a task in a streamlined way. Here we propose the Possum volumetric reconstruction framework which provides a selection of 2D to 3D image reconstruction routines allowing one to build workflows tailored to one’s specific requirements. The main components include routines for reconstruction with or without using external reference and solutions for typical issues encountered during the reconstruction process, such as propagation of the registration errors due to distorted sections. We validate the implementation using synthetic datasets and actual experimental imaging data derived from publicly available resources. We also evaluate efficiency of a subset of the algorithms implemented. The Possum framework is distributed under MIT license and it provides researchers with a possibility of building reconstruction workflows from existing components, without the need for low-level implementation. As a consequence, it also facilitates sharing and data exchange between researchers and laboratories.

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Section: Discussion and Summarymentioning

confidence: 99%

Possum—A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections

Majka

Wójcik

2015

Neuroinform

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“…We used a brain model from Brain Atlas Reconstructor (BAR) [21], [22] as a template for spline mapping. Morover, the template was validated by measuring the structure of additional nine rat brains.…”

Section: Brain Modelmentioning

confidence: 99%

“…We compared the scan of the rat brain from the atlas [21], [22] and the scanned rat brains. Rat brains were aligned to the atlas according to the smallest deviation.…”

Section: Model Validationmentioning

confidence: 99%

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Methods for Animal Brain Mapping

Tylš¹,

Krajča²,

Páleníček³

et al. 2018

RADIOENGINEERING

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Measurements of brain electrical activity in animals are essential for the validation of the pharmaco-effect of drugs. The way to evaluate these recordings should be comparable to that of EEG in humans. Methods that visualize the results of the measured EEG recording include brain mapping in two-dimensional or three-dimensional space. The most commonly used methods of interpolation techniques in humans are spherical splines and 3D splines. We measured nine brains of Wistar rats and compared them with a brain model from the atlas (Brain Atlas Reconstructor, BAR). We validated the brain model of Wistar rat for future use. We implemented a module in MATLAB 2015a for brain mapping, specifically, we implemented algorithms for spherical and 3D spline mapping. The root mean square error of the spherical spline method is 0.5943 in the case of testing signal and 0.6291/0.6388 in the case of real data estimation. The root mean square error of the 3D spline method is 0.4334 in the case of testing signal and 0.0849/0.0768 in the case of real data estimation. Our results show that the 3D spline method with the projection on sphere gives significantly better 3D potential map than spherical splines.

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“…However, it cannot satisfy researchers' demands for special tissues, especially not for biochemical analyses. As for brain atlases, different ones, with different methods 74,75 and disease foci, exist in digital formats, 76 but their use in new research is limited.…”

Section: Providing Brain Materials To Third Parties and Financial Sustmentioning

confidence: 99%

Why brain banking should be regarded as a special type of biobanking: ethical, practical, and data-management challenges

Nussbeck¹,

Wemheuer²,

Beier³

2015

BSAM

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Biobanking of the brain and other central nervous system materials, ie, brain banking (BB), provides an important research tool for understanding the causes of neurodegenerative and psychiatric diseases. Particularly with aging societies, there is an increasing need for molecular neuropathological research in this field. While there is an extensive debate on biobanking in general, the specific challenges that the procurement, processing, and storage of postmortem human brain tissue, and especially whole brains, raise are hardly ever considered systematically. This paper analyzes the peculiarities that make BB a distinct type of biobanking by combining the perspectives of neuropathology, medical informatics, and medical ethics. While ethical, practical, and data-management issues are often dealt with separately and the focus of such research is on only specific aspects of BB, this paper aims at an integrated analysis of the whole process. Six crucial steps in the BB workflow are analyzed: a) donor recruitment, b) follow-up during the donor's lifetime, c) postmortem brain donation, d) neuropathological diagnosis, e) research with brain tissue, and f) the provision of brain material to third parties. A comprehensive understanding of the challenges that BB raises is vital for making this practice more effective but also to counteract the current decline in brain-donation rates.

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3D Brain Atlas Reconstructor Service—Online Repository of Three-Dimensional Models of Brain Structures

Cited by 15 publications

References 32 publications

Possum—A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections

Possum—A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections

Methods for Animal Brain Mapping

Why brain banking should be regarded as a special type of biobanking: ethical, practical, and data-management challenges

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