scholarly journals CloudReg: Automatic Terabyte-Scale Cross-Modal Brain Volume Registration

2021 ◽  
Author(s):  
Vikram Chandrashekhar ◽  
Daniel J Tward ◽  
Devin Crowley ◽  
Ailey K Crow ◽  
Matthew A Wright ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Brain Magnetic Resonance Imaging ◽  
Light Sheet ◽  
Imaging Data ◽  
Micro Computed Tomography ◽  
Light Sheet Microscopy ◽  
Volume Registration ◽  
Scalable Analysis ◽  
Spatially Varying

AbstractQuantifying terabyte-scale multi-modal human and animal imaging data requires scalable analysis tools. We developed CloudReg, an open-source, automatic, terabyte-scale, cloud-based image analysis pipeline that pre-processes and registers cross-modal volumetric datasets with artifacts via spatially-varying polynomial intensity transform. CloudReg accurately registers the following datasets to their respective atlases: in vivo human and ex vivo macaque brain magnetic resonance imaging, ex vivo mouse brain micro-computed tomography, and cleared murine brain light-sheet microscopy.

Advances in imaging feto-placental vasculature: new tools to elucidate the early life origins of health and disease

2020 ◽  
pp. 1-11
Author(s):  
Yutthapong Tongpob ◽  
Caitlin Wyrwoll
Keyword(s):  
Ex Vivo ◽  
Light Sheet ◽  
Experimental Models ◽  
Cardiovascular Development ◽  
Micro Computed Tomography ◽  
Placental Function ◽  
Light Sheet Microscopy ◽  
Health And Disease ◽  
Insight Into

Abstract Optimal placental function is critical for fetal development, and therefore a crucial consideration for understanding the developmental origins of health and disease (DOHaD). The structure of the fetal side of the placental vasculature is an important determinant of fetal growth and cardiovascular development. There are several imaging modalities for assessing feto-placental structure including stereology, electron microscopy, confocal microscopy, micro-computed tomography, light-sheet microscopy, ultrasonography and magnetic resonance imaging. In this review, we present current methodologies for imaging feto-placental vasculature morphology ex vivo and in vivo in human and experimental models, their advantages and limitations and how these provide insight into placental function and fetal outcomes. These imaging approaches add important perspective to our understanding of placental biology and have potential to be new tools to elucidate a deeper understanding of DOHaD.

scholarly journals Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer

2021 ◽  
Author(s):  
Kelly Kersten ◽  
Kenneth H Hu ◽  
Alexis J Combes ◽  
Bushra Samad ◽  
Tory Harwin ◽  
...  
Keyword(s):  
T Cells ◽  
Cd8 T Cells ◽  
Light Sheet ◽  
Light Sheet Microscopy ◽  
Spatially Resolved ◽  
Hypoxic Conditions ◽  
Synaptic Interactions ◽  
Positive Feedback Circuit ◽  
Major Impediment

T cell exhaustion is a major impediment to anti-tumor immunity. However, it remains elusive how other immune cells in the tumor microenvironment (TME) contribute to this dysfunctional state. Here we show that the biology of tumor-associated macrophages (TAM) and exhausted T cells (Tex) in the TME is extensively linked. We demonstrate that in vivo depletion of TAM reduces exhaustion programs in tumor-infiltrating CD8+ T cells and reinvigorates their effector potential. Reciprocally, transcriptional and epigenetic profiling reveals that Tex express factors that actively recruit monocytes to the TME and shape their differentiation. Using lattice light sheet microscopy, we show that TAM and CD8+ T cells engage in unique long-lasting antigen-specific synaptic interactions that fail to activate T cells, but prime them for exhaustion, which is then accelerated in hypoxic conditions. Spatially resolved sequencing supports a spatiotemporal self-enforcing positive feedback circuit that is aligned to protect rather than destroy a tumor.

Multiphoton Light-sheet Microscopy at Optimal Pulse Frequency for Fast In Vivo Imaging

2020 ◽  
Author(s):  
Vincent Maioli ◽  
Antoine Boniface ◽  
Pierre Mahou ◽  
Júlia Ferrer Ortas ◽  
Lamiae Abdeladim ◽  
...  
Keyword(s):  
In Vivo Imaging ◽  
Light Sheet ◽  
Pulse Frequency ◽  
Light Sheet Microscopy

scholarly journals Coupling optogenetics and light-sheet microscopy to study signal transduction in vivo

2017 ◽  
Vol 145 ◽  
pp. S70-S71
Author(s):  
Prameet Kaur ◽  
Timothy E. Saunders ◽  
Nicholas Tolwinski
Keyword(s):  
Signal Transduction ◽  
Light Sheet ◽  
Light Sheet Microscopy

Functional in vivo imaging using fluorescence lifetime light sheet microscopy (Conference Presentation)

2019 ◽  
Author(s):  
Simon M. Ameer-Beg ◽  
Claire A. Mitchell ◽  
Simon P. Poland ◽  
Robert D. Knight ◽  
Guoqing Wang ◽  
...  
Keyword(s):  
Fluorescence Lifetime ◽  
In Vivo Imaging ◽  
Light Sheet ◽  
Light Sheet Microscopy

In vivo light‐sheet microscopy resolves localisation patterns of FSD1 , a superoxide dismutase with function in root development and osmoprotection

2020 ◽  
Vol 44 (1) ◽  
pp. 68-87 ◽  
Author(s):  
Petr Dvořák ◽  
Yuliya Krasylenko ◽  
Miroslav Ovečka ◽  
Jasim Basheer ◽  
Veronika Zapletalová ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Root Development ◽  
Light Sheet ◽  
Light Sheet Microscopy

scholarly journals In Vivo Tracking of Murine Adipose Tissue-Derived Multipotent Adult Stem Cells and Ex Vivo Cross-Validation

2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
Chiara Garrovo ◽  
Natascha Bergamin ◽  
Dave Bates ◽  
Daniela Cesselli ◽  
Antonio Paolo Beltrami ◽  
...  
Keyword(s):  
Stem Cells ◽  
Adipose Tissue ◽  
Optical Imaging ◽  
Adult Stem Cells ◽  
Near Infrared ◽  
Cross Validation ◽  
Ex Vivo ◽  
Imaging Data ◽  
Imaging Results

Stem cells are characterized by the ability to renew themselves and to differentiate into specialized cell types, while stem cell therapy is believed to treat a number of different human diseases through either cell regeneration or paracrine effects. Herein, an in vivo and ex vivo near infrared time domain (NIR TD) optical imaging study was undertaken to evaluate the migratory ability of murine adipose tissue-derived multipotent adult stem cells [mAT-MASC] after intramuscular injection in mice. In vivo NIR TD optical imaging data analysis showed a migration of DiD-labelled mAT-MASC in the leg opposite the injection site, which was confirmed by a fibered confocal microendoscopy system. Ex vivo NIR TD optical imaging results showed a systemic distribution of labelled cells. Considering a potential microenvironmental contamination, a cross-validation study by multimodality approaches was followed: mAT-MASC were isolated from male mice expressing constitutively eGFP, which was detectable using techniques of immunofluorescence and qPCR. Y-chromosome positive cells, injected into wild-type female recipients, were detected by FISH. Cross-validation confirmed the data obtained by in vivo/ex vivo TD optical imaging analysis. In summary, our data demonstrates the usefulness of NIR TD optical imaging in tracking delivered cells, giving insights into the migratory properties of the injected cells.

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