Sex matters: the MouseX DW-ALLEN Atlas for mice diffusion-weighted MR imaging DOI Creative Commons
Patricia Martínez-Tazo,

Alexandra Santos,

Mohamed Kotb Selim

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 27, 2023

Abstract Overcoming sex bias in preclinical research requires not only including animals of both sexes the experiments, but also developing proper tools to handle such data. Recent work revealed sensitivity diffusion-weighted MRI glia morphological changes response inflammatory stimuli, opening up exciting possibilities characterize inflammation a variety models pathologies, great majority them available mice. However, there are limited resources dedicated mouse imaging, like those required for data processing and analysis. To fill this gap, we build template structural diffusion contrasts, with anatomical annotation according Allen Mouse Brain Atlas, most detailed public resource brain investigation. achieve standardized resource, use large cohort vivo , include sexes. prove utility integrate imaging molecular data, demonstrate significant association between mean diffusivity from gene expression-based glial counting. need equitable representation, compared across warp fields needed match male-based template, our built Then, templates analysing mice obtained different ages, demonstrating that using creates spurious effects, present otherwise. All all, MouseX DW-ALLEN Atlas will be widely useful getting us one step closer healthcare. Graphical abstract

Language: Английский

ABBA, a novel tool for whole-brain mapping, reveals brain-wide differences in immediate early genes induction following learning DOI Creative Commons
Nicolas Chiaruttini,

Carlo Castoldi,

Linda Maria Requie

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 6, 2024

Abstract Unbiased characterization of whole-brain cytoarchitecture represents an invaluable tool for understanding brain function. For this, precise mapping histological markers from 2D sections onto 3D atlases is pivotal. Here, we present two novel software tools facilitating this process: Aligning Big Brains and Atlases (ABBA), designed to streamline the efficient registration reference atlases, BraiAn, integrated suite multi-marker automated segmentation, statistical analysis, data visualisation. Combining these tools, performed a comprehensive comparative study expression three most widely used immediate early genes (IEGs). Thanks their neural activity-dependent expression, IEGs have been decades as proxy activity generate unbiased following behaviour, but respective induction in response neuronal activation across entire remains unclear. To address question, systematically compared brain-wide cFos, Arc NPAS4, abundantly IEGs, different behavioural conditions related memory. Our results highlight major differences both distribution patterns, indicating that they do not represent equivalent areas or states, can provide instead complementary information.

Language: Английский

Citations

6
Bell Jar: A Semiautomated Registration and Cell Counting Tool for Mouse Neurohistology Analysis DOI Creative Commons

Alec L. R. Soronow,

Matthew W. Jacobs,

Richard G. Dickson

et al.

eNeuro, Journal Year: 2025, Volume and Issue: 12(2), P. ENEURO.0036 - 23.2025

Published: Feb. 1, 2025

For comprehensive anatomical analysis of a mouse brain, accurate and efficient registration the experimental brain samples to reference atlas is necessary. Here, we introduce Bell Jar, semiautomated solution that can align annotate tissue sections with structures from as well detect fluorescent signals cellular resolution (e.g., cell bodies or nuclei). Jar utilizes Mattes mutual information-directed B-spline transformations achieve precise alignments, even damaged sample tissues. While user input remains requirement for fine-tuning section matches, platform streamlines process, aiding rapid analyses in high-throughput neuroanatomy studies. As standalone desktop application user-friendly interface, Jar’s performance, which surpasses traditional manual existing automated methods, improve reproducibility throughput histological analyses.

Language: Английский

Citations

0
Construction of a Multimodal 3D Atlas for a Micrometer-Scale Brain–Computer Interface Based on Mixed Reality DOI
Hong Zhou, Zhiqiang Yan,

Wen-Yuan Gao

et al.

Current Medical Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 18, 2025

Language: Английский

Citations

0
SlicesMapi: An Interactive Three-Dimensional Registration Method for Serial Histological Brain Slices DOI

Zoutao Zhang,

Lingyi Cai,

Wenwei Li

et al.

Neuroinformatics, Journal Year: 2025, Volume and Issue: 23(2)

Published: April 16, 2025

Language: Английский

Citations

0
Sex matters: The MouseX DW-ALLEN Atlas for mice diffusion-weighted MR imaging DOI Creative Commons
Patricia Martínez-Tazo,

Alexandra Santos,

Mohamed Kotb Selim

et al.

NeuroImage, Journal Year: 2024, Volume and Issue: 292, P. 120573 - 120573

Published: March 21, 2024

Overcoming sex bias in preclinical research requires not only including animals of both sexes the experiments, but also developing proper tools to handle such data. Recent work revealed sensitivity diffusion-weighted MRI glia morphological changes response inflammatory stimuli, opening up exciting possibilities characterize inflammation a variety models pathologies, great majority them available mice. However, there are limited resources dedicated mouse imaging, like those required for data processing and analysis. To fill this gap, we build template structural diffusion contrasts, with anatomical annotation according Allen Mouse Brain Atlas, most detailed public resource brain investigation. achieve standardized resource, use large cohort vivo, include sexes. prove utility integrate imaging molecular data, demonstrate significant association between mean diffusivity from gene expression-based density. need equitable representation, compared across warp fields needed match male-based template, our built Then, templates analysing mice obtained different ages, demonstrating that using creates spurious effects, present otherwise. All all, MouseX DW-ALLEN Atlas will be widely useful getting us one step closer healthcare.

Language: Английский

Citations

1
An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain DOI Creative Commons
Sébastien Piluso, Csaba Verasztó, Harry Carey

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 8, 2024

ABSTRACT Brain atlases are essential for quantifying cellular composition in mouse brain regions. The Allen Institute’s Common Coordinate Framework version 3 (CCFv3) is widely used, delineating over 600 anatomical regions, but it lacks coverage the most rostral and caudal parts, including main olfactory bulb, cerebellum, medulla. Additionally, CCFv3 omits key cerebellar layers, its corresponding Nissl-stained reference volume not precisely aligned, limiting utilisability. To address these issues, we developed an extended atlas, Blue Project augmented (CCFv3aBBP), which includes a fully annotated improved Nissl aligned CCFv3. This enhanced atlas also features central nervous system annotation (CCFv3cBBP). Using this resource, 734 brains to produce average template, enabling updated distribution of neuronal soma positions. These data available as open-source broadening applications such alignment precision, cell type mapping, multimodal integration.

Language: Английский

Citations

0
Upscaling Mouse Spinal Cord Atlas for 3D Alignment DOI

X. Q. Feng,

Guangwei Zhang

Published: Oct. 18, 2024

Language: Английский

Citations

0
Sex matters: the MouseX DW-ALLEN Atlas for mice diffusion-weighted MR imaging DOI Creative Commons
Patricia Martínez-Tazo,

Alexandra Santos,

Mohamed Kotb Selim

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 27, 2023

Abstract Overcoming sex bias in preclinical research requires not only including animals of both sexes the experiments, but also developing proper tools to handle such data. Recent work revealed sensitivity diffusion-weighted MRI glia morphological changes response inflammatory stimuli, opening up exciting possibilities characterize inflammation a variety models pathologies, great majority them available mice. However, there are limited resources dedicated mouse imaging, like those required for data processing and analysis. To fill this gap, we build template structural diffusion contrasts, with anatomical annotation according Allen Mouse Brain Atlas, most detailed public resource brain investigation. achieve standardized resource, use large cohort vivo , include sexes. prove utility integrate imaging molecular data, demonstrate significant association between mean diffusivity from gene expression-based glial counting. need equitable representation, compared across warp fields needed match male-based template, our built Then, templates analysing mice obtained different ages, demonstrating that using creates spurious effects, present otherwise. All all, MouseX DW-ALLEN Atlas will be widely useful getting us one step closer healthcare. Graphical abstract

Language: Английский

Citations

0