CUBIC-f: An optimized clearing method for cell tracing and evaluation of neurite density in the salamander brain

Pinheiro, Tiago Novaes; Mayor, Ivy; Edwards, Steven J; Joven, Alberto; Kantzer, Christina Geraldine; Kirkham, Matthew; Simon, András

doi:10.1016/j.jneumeth.2020.109002

Cited by 9 publications

(8 citation statements)

References 28 publications

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“…As the use of whole-tissue imaging to address diverse scientific questions becomes increasingly prevalent ( Renier et al, 2014 ; Epp et al, 2015 ; Jing et al, 2018 ; Li et al, 2018 ; Pinheiro et al, 2021 ), it is imperative that analyses can flexibly meet the demands of these questions. Having noted the lack of a user-friendly and highly flexible registration tool, we developed an open-source tool to register images to custom atlases.…”

Section: Discussionmentioning

confidence: 99%

FASTMAP: Open-Source Flexible Atlas Segmentation Tool for Multi-Area Processing of Biological Images

Terstege

Oboh

Epp

2022

eNeuro

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To better understand complex systems, such as the brain, studying the interactions between multiple brain regions is imperative. Such experiments often require delineation of multiple brain regions on microscopic images based on preexisting brain atlases. Experiments examining the relationships of multiple regions across the brain have traditionally relied on manual plotting of regions. This process is very intensive and becomes untenable with a large number of regions of interest (ROIs). To reduce the amount of time required to process multi-region datasets, several tools for atlas registration have been developed; however, these tools are often inflexible to tissue type, only supportive of a limited number of atlases and orientation, require considerable computational expertise, or are only compatible with certain types of microscopy. To address the need for a simple yet extensible atlas registration tool, we have developed FASTMAP, a Flexible Atlas Segmentation Tool for Multi-Area Processing. We demonstrate its ability to register images efficiently and flexibly to custom mouse brain atlas plates, to detect differences in the regional numbers of labels of interest, and to conduct densitometry analyses. This open-source and user-friendly tool will facilitate the atlas registration of diverse tissue types, unconventional atlas organizations, and a variety of tissue preparations.

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Section: Discussionmentioning

confidence: 99%

FASTMAP: Open-Source Flexible Atlas Segmentation Tool for Multi-Area Processing of Biological Images

Terstege

Oboh

Epp

2022

eNeuro

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“…For example, the recent development of axolotl Fucci lines independently by both Duerr et al, as well as Cura Costa et al, allows for an unprecedented level of detail to understand cell cycle dynamics during axolotl tissue regeneration, 3,4 particularly in combination with either live imaging or the recently developed optical clearing protocols for salamander systems. [5][6][7][8] Leo Otsuki (IMP, Austria) provided an overview of how these novel imaging tools can be used to study cell cycle kinetics during axolotl spinal cord regeneration. The combination of advanced imaging and mathematical modeling by Emanuel Cura Costa and Osvaldo Chara led to the precise definition of an 800 μm zone of stem cell activation.…”

Section: The Wonders Of Regenerationmentioning

confidence: 99%

“…Salamanders are excellent vertebrate models to apply novel tools to study cell biological aspects of regeneration. For example, the recent development of axolotl Fucci lines independently by both Duerr et al, as well as Cura Costa et al, allows for an unprecedented level of detail to understand cell cycle dynamics during axolotl tissue regeneration, 3,4 particularly in combination with either live imaging or the recently developed optical clearing protocols for salamander systems 5‐8 . Leo Otsuki (IMP, Austria) provided an overview of how these novel imaging tools can be used to study cell cycle kinetics during axolotl spinal cord regeneration.…”

Section: The Wonders Of Regenerationmentioning

confidence: 99%

Meeting report: Salamander models in cross‐disciplinary biological research meeting

Masselink

Sandoval-Guzmán

Yun

2022

Developmental Dynamics

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The third annual meeting on “Salamander Models in Cross‐disciplinary Biological Research” took place online on August 2021, bringing together over 200 international researchers using salamanders as research models and encompassing diverse fields, ranging from Development and Regeneration through to Immunology, Pathogenesis, and Evolution. The event was organized by Maximina H. Yun (Center for Regenerative Therapies Dresden, Germany) and Tatiana Sandoval‐Guzmán (TU Dresden, Germany) with the generous support of the Deutsche Forschungsgemeinschaft, the Center for Regenerative Therapies Dresden, Technische Universität Dresden, and the Company of Biologists. Showcasing a number of emerging salamander models, innovative techniques and resources, and providing a platform for sharing both published and ongoing research, this meeting proved to be an excellent forum for exchanging ideas and moving research forwards. Here, we discuss the highlights stemming from this exciting scientific event.

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“…Many salamander tissues are optically transparent, and highly suited to live imaging. Further, several optical clearing methods have been adapted to the salamander system, enabling volumetric quantitative imaging ( Duerr et al, 2020 ; Masselink and Tanaka, 2020 ; Pinheiro et al, 2020 ; Subiran Adrados et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Salamander Insights Into Ageing and Rejuvenation

Yun

2021

Front. Cell Dev. Biol.

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Exhibiting extreme regenerative abilities which extend to complex organs and entire limbs, salamanders have long served as research models for understanding the basis of vertebrate regeneration. Yet these organisms display additional noteworthy traits, namely extraordinary longevity, indefinite regenerative potential and apparent lack of traditional signs of age-related decay or “negligible senescence.” Here, I examine existing studies addressing these features, highlight outstanding questions, and argue that salamanders constitute valuable models for addressing the nature of organismal senescence and the interplay between regeneration and ageing.

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CUBIC-f: An optimized clearing method for cell tracing and evaluation of neurite density in the salamander brain

Cited by 9 publications

References 28 publications

FASTMAP: Open-Source Flexible Atlas Segmentation Tool for Multi-Area Processing of Biological Images

FASTMAP: Open-Source Flexible Atlas Segmentation Tool for Multi-Area Processing of Biological Images

Meeting report: Salamander models in cross‐disciplinary biological research meeting

Salamander Insights Into Ageing and Rejuvenation

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