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Obtaining clearer and more detailed microscopic images deep within tissue has become a rich area of research in fields ranging from adaptive optics to photodynamic therapy. Visualising biological structures in vivo or non-invasively is a powerful strategy for discoveries in the live workings of our cells, tissues and organs. However, breaking the technological and biological barriers that traditionally limit imaging in deep tissue to the range of a few millimeters requires exceptional techniques and pioneering research developments.
Nature Communications, Communications Biology, Communications Engineering, npj Imaging and Scientific Reports are now inviting research Articles on the topic of microscopic imaging within deep tissue. This Collection will highlight Articles that involve new tools and emerging techniques for imaging at increased penetration depths within tissue as well as considering advances in conventional and state-of-the-art light microscopy techniques.
Topics of interest include but are not limited to: tools and techniques for microscopy in deep tissue, multimodal solutions for increasing penetration depth, and advancements in image processing. Reviews, Perspectives, and Comments covering these topics will also be considered for inclusion in the Collection. All submissions will be subject to the same review process and editorial standards as regular articles submitted to the contributing journals.
The authors present a rapid wavefront shaping system for fast, high-resolution imaging deep inside scattering tissue. It does this by optically acquiring the focusing score’s gradient, a method orders of magnitude faster than previous techniques.
Enhanced label-free multiphoton skin imaging uses phasor analysis to unmix key endogenous fluorophores, enabling mapping of molecular components in skin of varying pigmentation and metabolic states.
The authors developed a specialized objective lens that corrects GRIN lens aberrations, enabling in vivo, large–field-of-view, two-photon volumetric calcium imaging of more than 1,000 neurons deep within mouse brains.
3D ovarian elasticity mapping reveals distinct spatial elasticity patterns in follicles and corpora lutea, age-related changes, and potential correlations with cellular phenotypes and matrix composition.
Fluorescence microscopes lose over half the emitted light, limiting image clarity. Weidong Yang and colleagues here report the Paired-Objectives Photon Enhancement method to double photon capture, enhancing brightness and resolution in biological imaging.
This study presents LiteLoc, a lightweight and scalable AI model for efficient and accurate single molecule localization microscopy data analysis, bringing real-time deep-learning-based analysis to the era of high throughput super resolution imaging.
Madruga and colleagues present an open-source, miniature 2-photon microscope that can fit on a mouse’s head. Using this system, the authors perform high-resolution brain activity measurements in fine neuronal structures, which they can achieve even in conditions where the mouse is freely-moving within its cage.
This article presents structured illumination microscopy in deep tissue. With minor modifications to a two-photon microscope, the authors overcome scattering in dense biological samples, achieving 150 nm lateral resolution in depths down to 70 μm.
Three-photon in vivo imaging provides access to medial prefrontal cortex, hippocampus and spinal cord in mice at up to 1.7 mm depth of neurons, dendrites, spines, astrocytes and microglia.
Fung et al. use a multi-modal label-free 3D imaging platform to uncover morphological and biomolecular features in diabetic human kidney tissues such as glomerular volume, lipid saturation, optical redox ratio, and collagen fiber thickness.
Wei, Bai, Wang, and colleagues present HypnoS, a genetically-encoded fluorescent sensor for the real-time monitoring of intracellular adenosine (iAdo) in a cell type-specific manner. They monitor iAdo dynamics during seizures or sleep-wake cycles with high spatiotemporal resolution in the brain of living animals.
Neural data analysis algorithms capable of tracking neuronal signals from one-photon functional imaging data longitudinally and reliably are still lacking. Here authors developed CaliAli, a tool for extracting calcium signals across multiple days. Validated with optogenetic tagging, dual-color imaging, and place cell data, CaliAli demonstrated stable neuron tracking for up to 99 days.
Integrated solutions for the analysis of complex 3D and live cell images remain scarce. Here, the authors present Cecelia, an image analysis toolbox based on R and Python, which enables researchers to quantify large scale tissue sections as well as live cell imaging data. Its modular design makes it applicable to a variety of use cases.
Optical aberrations can hinder the quality of imaging outputs, affecting research across many disciplines. Here, using the tilt-tilt correlation from the optical memory effect, the authors are able to correct aberrations in challenging conditions, including highly aberrated or moving samples.
Strategies to synthesize a chemiluminescence (CL) emission unimolecular skeleton in the second near-infrared window (NIR-II) and a unimolecular probe with direct duplex NIR-II [CL/fluorescence (FL)] emission are lacking. Here, the authors employ modular synthesis routes to construct a series of directly activated NIR-II CL emission unimolecular probes with a maximum emission wavelength of up to 1060 nm, and use them for real-time and continuous detection of the superoxide anion generated in acetaminophen induced liver injury under both NIR-II CL and NIRII FL imaging channels.
INSIHGT is an affordable, non-destructive and accessible 3D spatial biology method that maps diverse biomolecules deep within tissues, such as proteins and RNA, thus advancing the understanding of complex biological systems on a multi-omics level.
Rui Li, Gabriel della Maggiora and co-authors present a deep learning approach for attenuating diffraction and optical imperfections in light microscopy images. By incorporating the underlying physics of light propagation in microscopy into the loss function and designing a conditional diffusion model, they obtained improved performance compared to the state-of-the-art.
Haoyang Li, Quan Lu, Zhong Wang, and colleagues present a cost-effective and fast 3D random-access confocal microscopy. They demonstrate its performance of fluorescent particles and live Hela cells.
The extrusion of large extracellular vesicles is an important mechanism that facilitates cell-to-cell communication and maintains homoeostasis. Here, Atkin-Smith et al. use intravital microscopy to directly visualize the formation of large extracellular vesicles in bone marrow.
Microscopy exploits light scattering to image biological tissues, but heterogeneities distort wave trajectories, creating a foggy image. A digital approach is proposed to harness these complex paths and reveal the inner structure of opaque media.