Article
Biotechnology & Applied Microbiology
Jiwon Woo, Eunice Yoojin Lee, Mirae Lee, Seockmo Ku, Jeong-Yoon Park, Yong Eun Cho
Summary: The advent of tissue clearing methods and high-resolution imaging techniques has enabled the visualization of three-dimensional structures in unprecedented detail. This study presents two simple assays, PACA-Light and PACA-Glow, to quantify the transparency of multiple cleared tissues simultaneously. The study compares 28 tissue clearing protocols on rodent brains and reveals regional differences in tissue transparency.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Luis R. Oliveira, Ricardo M. Ferreira, Maria R. Pinheiro, Hugo F. Silva, Valery V. Tuchin, Luis M. Oliveira
Summary: Sequential optical immersion clearing treatments can increase tissue transparency and have high interest for clinical applications. This study found that a saline immersion can reverse the clearing effect in lung tissue, while a second treatment with the optical clearing agent can double the transparency, indicating a conversion of bound water to mobile water during the first treatment.
JOURNAL OF BIOPHOTONICS
(2023)
Article
Biochemical Research Methods
Hugo F. Silva, Ines S. Martins, Alexei A. Bogdanov, Valery V. Tuchin, Luis M. Oliveira
Summary: The recent increase in interest in the application of radiology contrasting agents to create transparency in biological tissues has led to the need for evaluating the diffusion properties of these agents. This study evaluated and compared the diffusion properties of gadobutrol and glycerol in skeletal muscle, showing that gadobutrol has a faster diffusion in the muscle despite its higher molar mass.
JOURNAL OF BIOPHOTONICS
(2023)
Review
Anatomy & Morphology
Z. Guo, Y. Zheng, Y. Zhang
Summary: This article provides a systematic overview of the progress in CLARITY techniques for tissue clearing, categorizing them into active CLARITY, passive CLARITY, and a combination of active and passive CLARITY. The review summarizes the advantages and limitations of these methods, helping researchers select suitable tissue clearing methods for their experimental samples more quickly and effectively, while also providing insights for improving the techniques.
FOLIA MORPHOLOGICA
(2022)
Article
Optics
Hiroshi Ohno, Takashi Usui
Summary: Unsupervised neural network ray tracing (NNRT) is proposed to calculate light ray paths connecting given points in a gradient-index medium. Using Maxwell's fisheye lens as an example, NNRT is shown to accurately trace ideal light ray paths passing through given points.
Article
Biochemistry & Molecular Biology
Youngjae Ryu, Yoonju Kim, Hye Ryeong Lim, Hyung-Joon Kim, Byong Seo Park, Jae Geun Kim, Sang-Joon Park, Chang Man Ha
Summary: Recent advances in optical clearing techniques have improved deep tissue imaging by reducing light scattering and absorption. However, current methods have limitations and are complex. Researchers have developed a one-step tissue clearing solution called AICI that can rapidly clear and match refractive index, allowing for imaging without additional processing. AICI has low viscosity and remains fluid for extended periods of time, making it useful for various optical imaging applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Zong-Yi Zhan, Yi-Ru Huang, Lu-Wei Zhao, Ya-Dan Quan, Zi-Jing Li, Di-Fang Sun, Ya-Li Wu, Hao-Yuan Wu, Zi-Tian Liu, Kai-Li Wu, Yu-Qing Lan, Min-Bin Yu
Summary: This study used a combination of tissue cleaning technique and retrograde trans-synaptic viral tracing to observe changes in retinorecipient regions connected to retinal ganglion cells in mice after optic nerve injury. The findings demonstrate the usefulness of this approach for evaluating optic nerve injury and regeneration.
NEURAL REGENERATION RESEARCH
(2023)
Article
Multidisciplinary Sciences
Elizabeth J. Alessio, Dao-Qi Zhang
Summary: The CLARITY method has been adapted for whole-mount mouse retinas, improving the quality of immunostaining and imaging for retinal neurons and glial cells. By rendering the retina more optically transparent and preserving fine structures of retinal neurons and their proteins, CLARITY allows for high-resolution imaging of retinal neurons and their subcellular structures in whole-mount preparation.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Review
Multidisciplinary Sciences
Tingting Yu, Jingtan Zhu, Dongyu Li, Dan Zhu
Summary: Advanced optical methods combined with various probes have enabled molecular imaging within living cells, but improving imaging resolution to the subcellular level is a major challenge for larger tissues and in vivo studies. Tissue optical clearing techniques offer innovative ways to perform deep-tissue imaging, with various methods developed based on similar physical principles but using different chemical approaches. This includes refractive index matching and chemical treatments to reduce scattering and absorption for deeper tissue imaging.
Article
Neurosciences
Henriette Rusch, Malte Brammerloh, Jens Stieler, Mandy Sonntag, Siawoosh Mohammadi, Nikolaus Weiskopf, Thomas Arendt, Evgeniya Kirilina, Markus Morawski
Summary: The accessibility of new wide-scale multimodal imaging techniques has led to the emergence of numerous tissue clearing techniques. This study compares seven different tissue clearing approaches for aged human brain tissue blocks (>5 mm) to identify the most practical and efficient method. The results show that combining the CLARITY or iDISCO techniques with specific imaging setups is the best approach for clearing aged human brain tissue and generating 3D microscopic images.
Article
Biochemical Research Methods
Irina Yu Yanina, Yohei Tanikawa, Elina A. Genina, Polina A. Dyachenko, Daria K. Tuchina, Alexey N. Bashkatov, Leonid E. Dolotov, Yana Tarakanchikova, Georgy S. Terentuk, Nikita A. Navolokin, Alla B. Bucharskaya, Galina N. Maslyakova, Yasunobu Iga, Shinichi Takimoto, Valery V. Tuchin
Summary: This study focuses on the development of technology for optical clearing (OC) of abdominal adipose tissue in vivo using hyperosmotic optical clearing agents (OCAs). The results demonstrate that OCAs can effectively clear adipose tissue and induce cell necrosis to a certain extent, both in ex vivo and in vivo experiments.
JOURNAL OF BIOPHOTONICS
(2022)
Article
Chemistry, Analytical
Niall M. C. Mulkerns, William H. Hoffmann, Ian D. Lindsay, Henkjan Gersen
Summary: This study presents a ray tracing model for on-chip backscattering interferometry with a semicircular cross-section. Comparing with experimental data, it is found that the current semicircular geometry cannot explain the results, indicating the need for further clarification on the optical mechanisms behind different modalities of backscattering interferometry.
Article
Engineering, Biomedical
Alyssa J. Huntington, Barath Udayasuryan, Pang Du, Scott S. Verbridge, Steven D. Abramowitch, Raffaella De Vita
Summary: Smooth muscle fibers in the vagina, along with the nerve fibers controlling them, play a crucial role in maintaining vaginal length and tone. Vaginal smooth muscle is typically arranged in concentric layers, with differences in orientation observed between the proximal and distal regions. Microstructural analyses are important for understanding the physiological function and pathological changes of the vagina.
ANNALS OF BIOMEDICAL ENGINEERING
(2022)
Article
Materials Science, Multidisciplinary
Maria Matiatou, Panagiotis Giannios, Spyridon Koutsoumpos, Konstantinos G. Toutouzas, George C. Zografos, Konstantinos Moutzouris
Summary: The experimental determination of refractive index for eleven different human tissue types using a prism-coupling refractometer and a simple Cauchy model is reported in this study. The model accurately reproduces the experimental data and enables prediction of tissue refractive index in the entire visible and near-infrared spectral range, as well as estimation of dispersion-related parameters like group velocity dispersion.
RESULTS IN PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Qingpeng Zhang, Yi Tan, Ge Ren, Tao Tang
Summary: The method proposed in this paper utilizes refractive index steps for ray tracing, achieving high efficiency and precision in areas with rapid or slow refractive index changes. Through calculation examples, it has been shown to achieve tracking accuracy of 10(-5) mm, outperforming traditional methods in terms of speed and precision.
APPLIED SCIENCES-BASEL
(2021)
Article
Biology
Peter C. Petersen, Rune W. Berg
Review
Neurosciences
Rune W. Berg
FRONTIERS IN NEURAL CIRCUITS
(2017)
Article
Mathematical & Computational Biology
Catalina Vich, Rune W. Berg, Antoni Guillamon, Susanne Ditlevsen
FRONTIERS IN COMPUTATIONAL NEUROSCIENCE
(2017)
Editorial Material
Physics, Multidisciplinary
Rune W. Berg, Marius Tving Stauning, Jakob Balslev Sorensen, Henrik Jahnsen
Editorial Material
Neurosciences
Rune W. Berg
FRONTIERS IN NEURAL CIRCUITS
(2018)
Article
Neurosciences
Jean-Francois Perrier, Hanne B. Rasmussen, Lone K. Jorgensen, Rune W. Berg
FRONTIERS IN NEURAL CIRCUITS
(2018)
Article
Multidisciplinary Sciences
Marija Radosevic, Alex Willumsen, Peter C. Petersen, Henrik Linden, Mikkel Vestergaard, Rune W. Berg
NATURE COMMUNICATIONS
(2019)
Article
Neurosciences
Simon Henmar, Erik B. Simonsen, Rune W. Berg
JOURNAL OF NEUROPHYSIOLOGY
(2020)
Article
Neurosciences
Henrik Linden, Rune W. Berg
Summary: This study explores the central pattern generators (CPGs) in the spinal cord and emphasizes the importance of firing rate distributions in understanding their organization. It suggests that including recurrent inhibition in models is crucial for achieving firing rate distributions consistent with experimental observations.
FRONTIERS IN HUMAN NEUROSCIENCE
(2021)
Article
Engineering, Biomedical
Kunyang Sui, Marcello Meneghetti, Jaspreet Kaur, Roar Jakob Fleng Sorensen, Rune W. Berg, Christos Markos
Summary: This study presents the development of two flexible polymer optical fibers for efficient neuromodulation, featuring integrated microfluidic channels and an ultra-high numerical aperture. The proposed fibers have a larger illumination area and reduced bending stiffness compared to commercial silica fibers. Experimental results demonstrate their potential use as optical waveguides and in fiber photometry applications, paving the way for next-generation functional optical fibers in neuroscience.
JOURNAL OF NEURAL ENGINEERING
(2022)
Article
Multidisciplinary Sciences
Jaspreet Kaur, Rune W. Berg
Summary: Targeting specific subtypes of interneurons in the spinal cord is often limited to a small group of genetic model animals. However, using adeno-associated virus (AAV) to deliver endogenous enhancers and promoters has shown promise in expressing specific subtypes of neurons in the forebrain of wild-type animals. This study tested the specificity and efficiency of the mDlx enhancer in targeting inhibitory interneurons in the lumbar spinal cord of wild-type rats using AAV serotype 2 (AAV2), as well as the expression and specificity of the CamKIIa and hSynapsin promoters using AAV serotype 9 (AAV9).
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Henrik Linden, Peter C. Petersen, Mikkel Vestergaard, Rune W. Berg
Summary: The study reveals that neurons in the lumbar spinal cord perform a low-dimensional 'rotation' in neural space during rhythmic movements, rather than exhibiting alternating activity. This rotation correlates with muscle force and perturbation of the trajectory can modify motor behavior.
Review
Physiology
Rune W. Berg, Alex Willumsen, Henrik Linden
CURRENT OPINION IN PHYSIOLOGY
(2019)
Article
Biology
Peter C. Petersen, Rune W. Berg
