Atlas-based imaging data analysis tool for quantitative mouse brain histology (AIDAhisto)

Pallast, Niklas; Wieters, Frederique; Fink, Gereon R.; Aswendt, Markus

doi:10.1016/j.jneumeth.2019.108394

Cited by 21 publications

(25 citation statements)

References 22 publications

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“…In order to efficiently compare the lesion size and location, we applied a detailed atlas registration workflow [22,23], which provided unbiased and automated lesion mapping, connectivity analysis, and histology. For the stroke segmentation, we used the T2-weighted MRI (T2WI), which according to a recent meta-analysis, serves as an effective noninvasive assessment of infarct size during the first 2 weeks after the onset of ischemia [24].…”

Section: Lesion Size and Locationmentioning

confidence: 99%

Lesion Size- and Location-Dependent Recruitment of Contralesional Thalamus and Motor Cortex Facilitates Recovery after Stroke in Mice

Aswendt

Pallast

Wieters

et al. 2020

Transl. Stroke Res.

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Brain lesions caused by cerebral ischemia or hemorrhage lead to a local breakdown of energy homeostasis followed by irreversible cell death and long-term impairment. Importantly, local brain lesions also generate remote functional and structural disturbances, which contribute to the behavioral deficit but also impact the recovery of function. While spontaneous recovery has been associated with endogenous repair mechanisms at the vascular, neural, and immune cell levels, the impact of structural plasticity on sensory-motor dysfunction and recovery thereof remains to be elucidated by longitudinal imaging in a mouse model. Here, we applied behavioral assessments, in vivo fiber tracking, and histological validation in a photothrombotic stroke mouse model. Atlas-based whole-brain structural connectivity analysis and ex vivo histology revealed secondary neurodegeneration in the ipsilesional brain areas, mostly in the dorsal sensorimotor area of the thalamus. Furthermore, we describe for the first time a lesion size-dependent increase in structural connectivity between the contralesional primary motor cortex and thalamus with the ipsilesional cortex. The involvement of the contralesional hemisphere was associated with improved functional recovery relative to lesion size. This study highlights the importance of in vivo fiber tracking and the role of the contralesional hemisphere during spontaneous functional improvement as a potential novel stroke biomarker and therapeutic targets. Electronic supplementary material The online version of this article (10.1007/s12975-020-00802-3) contains supplementary material, which is available to authorized users.

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Section: Lesion Size and Locationmentioning

confidence: 99%

Lesion Size- and Location-Dependent Recruitment of Contralesional Thalamus and Motor Cortex Facilitates Recovery after Stroke in Mice

Aswendt

Pallast

Wieters

et al. 2020

Transl. Stroke Res.

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“…Several other groups have proposed tools for analysis of 2D mouse brain section images, without the need for 3D reconstruction (Furth et al, 2018;Xiong et al, 2018); however, the requirement for coding knowledge restricts the accessibility of these methods. The AIDAhisto tool enable atlas based quantifications but lack multi-angle adjustment (Pallast et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images

Groeneboom

Yates

Puchades

et al. 2020

Front. Neuroinform.

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With recent technological advances in microscopy and image acquisition of tissue sections, further developments of tools are required for viewing, transforming, and analyzing the ever-increasing amounts of high-resolution data produced. In the field of neuroscience, histological images of whole rodent brain sections are commonly used for investigating brain connections as well as cellular and molecular organization in the normal and diseased brain, but present a problem for the typical neuroscientist with no or limited programming experience in terms of the pre-and post-processing steps needed for analysis. To meet this need we have designed Nutil, an open access and stand-alone executable software that enables automated transformations, postprocessing, and analyses of 2D section images using multi-core processing (OpenMP). The software is written in C++ for efficiency, and provides the user with a clean and easy graphical user interface for specifying the input and output parameters. Nutil currently contains four separate tools: (1) A transformation toolchain named "Transform" that allows for rotation, mirroring and scaling, resizing, and renaming of very large tiled tiff images. (2) "TiffCreator" enables the generation of tiled TIFF images from other image formats such as PNG and JPEG. (3) A "Resize" tool completes the preprocessing toolset and allows downscaling of PNG and JPEG images with output in PNG format. (4) The fourth tool is a post-processing method called "Quantifier" that enables the quantification of segmented objects in the context of regions defined by brain atlas maps generated with the QuickNII software based on a 3D reference atlas (mouse or rat). The output consists of a set of report files, point cloud coordinate files for visualization in reference atlas space, and reference atlas images superimposed with color-coded objects.

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“…Advances in digital-based atlases ( Hjornevik et al, 2007 ; Lein et al, 2007 ) set the stage for the development of tools for registering histology to atlas reference spaces ( Kopec et al, 2011 ; Pallast et al, 2019 ). Atlas registration along with the quantification of brain region populations for labeled cells are critical steps for accurate post-imaging analysis.…”

Section: Introductionmentioning

confidence: 99%

“…Atlas registration along with the quantification of brain region populations for labeled cells are critical steps for accurate post-imaging analysis. Atlas registration involves a warping mechanism to align histology sections onto an idealized atlas ( Kopec et al, 2011 ; Shamash et al, 2018 ; Pallast et al, 2019 ; Bourgeois et al, 2021 ; Claudi et al, 2021 ). Deformations, angled images from non-zero anterior-posterior or medial-lateral tilt, and other imperfections in the slice image can complicate the warping process that is necessary to map sections to the atlas space.…”

Section: Introductionmentioning

confidence: 99%

A Semi-Automated Workflow for Brain Slice Histology Alignment, Registration, and Cell Quantification (SHARCQ)

Lauridsen

Prevost

et al. 2022

eNeuro

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Atlas-based imaging data analysis tool for quantitative mouse brain histology (AIDAhisto)

Cited by 21 publications

References 22 publications

Lesion Size- and Location-Dependent Recruitment of Contralesional Thalamus and Motor Cortex Facilitates Recovery after Stroke in Mice

Lesion Size- and Location-Dependent Recruitment of Contralesional Thalamus and Motor Cortex Facilitates Recovery after Stroke in Mice

Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images

A Semi-Automated Workflow for Brain Slice Histology Alignment, Registration, and Cell Quantification (SHARCQ)

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