High-resolution 3D Microscopy Research Articles

Simple high-resolution 3D microscopy by a dielectric microsphere: a proof of concept.

We present a simple high-resolution approach for 3D and quantitative phase imaging (QPI). Our method makes the most of a glass microsphere (MS) for microscopy and a glass plate for lateral shearing self-referencing interferometry. The single MS serves all the functions of a microscope objective (MO) in digital holographic microscopy (DHM) while offering the advantages of compactness, lightness, and affordability. A proof-of-concept experiment is performed on a standard diffraction grating, and various effective parameters on the imaging performance are investigated. The results are validated by atomic force microscopy and Mirau-DHM, and 3D morphometric information of the sample under inspection is obtained. The technique is then applied for 3D quantitative measurement and visualization of a human red blood cell, proving the principle of our easy-to-implement and vibration-immune arrangement for high-contrast label-free QPI of biological samples, and its utility in cell morphology, identification, and classification.

Thickness, Adhesion and Microscopic Analysis of the Surface Structure of Single-Layer and Multi-Layer Metakaolin-Based Geopolymer Coatings

This work is focused on creating coating layers made of a metakaolin-based geopolymer suspensions (GP)-formed Al matrix modified using H3PO4 acid with Al(OH)3 in isopropyl alcohol, named GP suspension I, and H3PO4 acid with nano Al2O3 in isopropyl alcohol, named GP suspension J. The selected GP suspensions were applied on aluminum and steel underlying substrates as single-layer coatings and multi-layer coatings, where multi-layer coatings included three and five layers that were polymerized by a curing process. Curing was divided into two types with every layer curing process and final layer curing process. For both GP suspensions I and J, the effect of the number of layers and the type of substrate on adhesion was investigated. The prepared samples on underlying substrates were characterized on the microscopy analysis including SEM for high-resolution images and 3D laser confocal microscopy (CLSM) for the 3D visualization of the coatings structure. Microscopy analysis showed structural defects such as porosity, cracks and peeling, which increase with a greater number of applied layers. However, these defects were only evident on a micro scale and did not seem to be fatal for the performance of the surface stability. The EDS mapping of the prepared layer showed inhomogeneity in the distribution of elements caused by the brush application. A grid test and thickness measurement were performed to complete the microscopy analysis. The grid test confirmed a very high adhesion of GP coatings on the aluminum substrate with a rating of one (only in one case was there a rating of two) and a lower adhesion on the steel substrate with the most frequent rating of three (in one case, there were ratings of two and one). The thickness measurement proved a noticeably thicker thickness of the prepared layer on the Fe substrate compared to the Al substrate by 20%–30% in the case of suspension I and by 70%–10% in the case of suspension J. The thickness of the layer also showed a dependence on the method of application and curing, as a thicker layer was always achieved when curing after the final layer of the GP suspension, compared to curing after each applied layer. The resulting single-layer and multi-layer thicknesses ranged from approx. 7 to 30 µm for suspension I and from approx. 3 to 11 µm for suspension J. A non-linear increase in thickness was also evident from the thickness measurement data.

Ebola Virus Uses Tunneling Nanotubes as an Alternate Route of Dissemination.

Ebola virus (EBOV) disease is marked by rapid virus replication and spread. EBOV enters the cell by macropinocytosis and replicates in the cytoplasm, and nascent virions egress from the cell surface to infect neighboring cells. Here, we show that EBOV uses an alternate route to disseminate: tunneling nanotubes (TNTs). TNTs, an actin-based long-range intercellular communication system, allows for direct exchange of cytosolic constituents between cells. Using live, scanning electron, and high-resolution quantitative 3-dimensional microscopy, we show that EBOV infection of primary human cells results in the enhanced formation of TNTs containing viral nucleocapsids. TNTs promote the intercellular transfer of nucleocapsids in the absence of live virus, and virus could replicate in cells devoid of entry factors after initial stall. Our studies suggest an alternate model of EBOV dissemination within the host, laying the groundwork for further investigations into the pathogenesis of filoviruses and, importantly, stimulating new areas of antiviral design.

Cleaning testing of nineteenth-century plaster surface models with thin polyacrylamide-based gel layers attached to flexible polyethylene films

This paper explores the cleaning efficacy of polyethylene-supported 15-min photo-crosslinked poly (acrylamide-co-benzophenone) surface-attached gels (SAGs) on gypsum plaster surface models inspired by nineteenth-century casts. Cleaning tests were performed on plaster surface models with and without organic and inorganic coatings, which had been exposed to accelerated ageing by heat, humidity, and light after artificial soiling. The specific types of SAG systems were selected based on their water loading and dehydration capacities. The SAGs were loaded with customized solutions and applied on the plaster models for one minute. Cleaning efficacy was evaluated with visible reflectance, UV fluorescence photography, scanning electron microscopy, colorimetry, UV/Vis spectrophotometry, glossimetry, high resolution 3D microscopy, attenuated total reflection Fourier transform infrared spectroscopy and 2D Fourier transform infrared imaging. The SAGs provided fast and minimal wetting of the substrates, prevented excessive liquid spreading and allowed the effective liquid contact with the soiled gypsum plaster surface. A striking removal of soils from the gypsum plaster surface models was observed, which suggests convenient application of the SAG systems for the cleaning of historical plaster objects.

Fueling the Simulation Machine: Considerations for High-Resolution 3D Microscopy to Support Computational Modeling in Battery Research

To meet the rapidly evolving energy needs of a growing population, energy storage and conversion devices such as batteries must rapidly evolve as well. Battery materials and other functional energy materials derive their properties not from their static state, but from how they interact with other materials in their service environment. Furthermore, the microstructure of these materials strongly dictates their performance and how they interact with other components (like electrolytes, binders, etc). In order to accelerate this development cycle, researchers are increasingly integrating computational modeling into their materials and device development efforts.Computational analysis is progressing to the point where simulations can incorporate real material microstructures, simulate statistically equivalent structures, and predict performance changes based on changes to these microstructures. At the same time experimental techniques have emerged that can deliver representative volumes of high-quality, high-resolution 3D microstructural images from real devices and materials. The interplay between advanced computational analysis and evolving characterization capabilities means we are rapidly approaching the realization of the “materials by design” paradigm where new materials are designed and tested digitally with input and validation provided by advanced materials characterization techniques. Within this paradigm, however, it is critical that the experimental techniques provide accurate, realistic, and representative input to the computational models. In the case of microstructural information, this means generating 3-dimensional images that accurately represents the materials in question.One key example of this is for materials, like battery materials and electrodes, which contain micro- and nano-scale porosity. Acquiring image data that can reproduce real material properties and feed accurate simulations is challenging and relies on satisfying several conditions. For example, the volume must be representative of the “bulk” material microstructure. The (2D) image resolution must capture the relevant scope of material features, and the 3D image must accurately represent the material in all 3 dimensions and at appropriate length scales. The focused-ion beam scanning electron microscope (FIB-SEM) is capable of imaging these micro- and nano-scale pore networks in 3D but care must be taken when considering these experiments, especially when the intent is to use the images to feed computational models.We present here a review of the factors researchers must consider when tackling these demanding tasks and highlight experimental recommendations for leveraging FIB-SEM tomography to produce the most relevant imaging data in this context. We use a lithium-ion battery cathode as a test case to demonstrate this approach, but the outcome and methods can be leveraged across the materials research space and beyond.

Subcellular Specialization of 3D Mitochondrial Morphology and Mitochondria‐Lipid Droplet Interactivity is Associated with Proximity to Oxygen Supply in Muscle Cells

Advancements in imaging technology have considerably expanded our capacity to investigate cell biology, and our laboratory has recently employed high-resolution 3D microscopy to explore the subcellular structures and organelle-organelle interactions that support muscle metabolism. While this initial work has demonstrated that mitochondrial structure and mitochondria-organelle interactivity are regulated according to muscle cell type, it remains unclear how cellular metabolism is supported by the subcellular specialization of mitochondria. Certainly, several subcellular clusters of mitochondria have been identified within muscle cells, and these groups of mitochondria are often categorized according to their proximity to other cellular components (i.e. “intermyofibrillar” or “paravascular”). However, it is unknown how 3D mitochondrial morphology and organelle interactivity is altered to support the varying functional demands of different subcellular regions. Here, we combine 3D focused-ion beam scanning electron microscopy (FIB-SEM) with machine learning programs to quantify individual mitochondrial structure and organelle interactivity within large subcellular volumes (~8,000 µm3) (Fig. 1a-c). Using this high-throughput approach, we evaluate over 700 individual mitochondria per cell and leverage the statistical power of this large data set to identify 3D spatial relationships among multiple subcellular structures. We find that mitochondrial surface area to volume ratio (15.5±0.25 µm-1) is significantly correlated (R2= 0.39) to the minimal distance to capillary, but not distance to sarcolemma (R2= 0.02) (Fig. 1d). Further analysis revealed that mitochondria-organelle interactivity is also closely related to subcellular localization. Specifically, mitochondria within close proximity (<5 µm) to capillaries (paravascular) are ~3-fold more likely to make contact with lipid droplets compared to mitochondria located in other subcellular regions (Fig. 1e). Moreover, the paravascular mitochondria in contact with lipid droplets have 75% greater volume (1.4±0.07 µm3) compared to those not connected to lipid droplets (0.8±0.03 µm3). These preliminary analyses suggest that mitochondria in close proximity to the muscle oxygen supply, but not cell boundary, exhibit distinct 3D morphology and organelle interactivity patterns that may function to support metabolism and other cellular processes.

Variability in stem taper surface topography affects the degree of corrosion and fretting in total hip arthroplasty

Degradation at the modular head-neck interface in total hip arthroplasty (THA) is predominately expressed in the form of corrosion and fretting, potentially causing peri-prosthetic failure by adverse reactions to metal debris. This retrieval study aimed to quantify variations in stem taper surface topographies and to assess the influence on the formation of corrosion and/or fretting in titanium alloy stem tapers combined with metal and ceramic heads. Four hip stem designs (Alloclassic, CLS, Bicontact and SL-Plus) were characterized using high-resolution 3D microscopy, and corrosion and fretting were rated using the Goldberg scoring scheme. Quantification of the taper surface topographies revealed a high variability in surface characteristics between threaded stem tapers: Alloclassic and CLS tapers feature deeply threaded trapezoid-shaped profiles with thread heights over 65 µm. The sawtooth-shaped Bicontact and triangular SL-Plus taper are characterized by low thread heights below 14 µm. Significantly lower corrosion and fretting scores were observed in lightly threaded compared to deeply threaded tapers in ceramic head combinations. No significant differences in corrosion or fretting scores with thread height were found in pairings with metal heads. Understanding the relationship between stem taper surface topography and the formation of corrosion and fretting could help to improve the performance of modern THAs and lead to longer-lasting clinical results.

PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies

BackgroundBioimaging techniques offer a robust tool for studying molecular pathways and morphological phenotypes of cell populations subjected to various conditions. As modern high-resolution 3D microscopy provides access to an ever-increasing amount of high-quality images, there arises a need for their analysis in an automated, unbiased, and simple way. Segmentation of structures within the cell nucleus, which is the focus of this paper, presents a new layer of complexity in the form of dense packing and significant signal overlap. At the same time, the available segmentation tools provide a steep learning curve for new users with a limited technical background. This is especially apparent in the bulk processing of image sets, which requires the use of some form of programming notation.ResultsIn this paper, we present PartSeg, a tool for segmentation and reconstruction of 3D microscopy images, optimised for the study of the cell nucleus. PartSeg integrates refined versions of several state-of-the-art algorithms, including a new multi-scale approach for segmentation and quantitative analysis of 3D microscopy images. The features and user-friendly interface of PartSeg were carefully planned with biologists in mind, based on analysis of multiple use cases and difficulties encountered with other tools, to offer an ergonomic interface with a minimal entry barrier. Bulk processing in an ad-hoc manner is possible without the need for programmer support. As the size of datasets of interest grows, such bulk processing solutions become essential for proper statistical analysis of results. Advanced users can use PartSeg components as a library within Python data processing and visualisation pipelines, for example within Jupyter notebooks. The tool is extensible so that new functionality and algorithms can be added by the use of plugins. For biologists, the utility of PartSeg is presented in several scenarios, showing the quantitative analysis of nuclear structures.ConclusionsIn this paper, we have presented PartSeg which is a tool for precise and verifiable segmentation and reconstruction of 3D microscopy images. PartSeg is optimised for cell nucleus analysis and offers multi-scale segmentation algorithms best-suited for this task. PartSeg can also be used for the bulk processing of multiple images and its components can be reused in other systems or computational experiments.

A Curvature-Enhanced Random Walker Segmentation Method for Detailed Capture of 3D Cell Surface Membranes.

High-resolution 3D microscopy is a fast advancing field and requires new techniques in image analysis to handle these new datasets. In this work, we focus on detailed 3D segmentation of Dictyostelium cells undergoing macropinocytosis captured on an iSPIM microscope. We propose a novel random walker-based method with a curvature-based enhancement term, with the aim of capturing fine protrusions, such as filopodia and deep invaginations, such as macropinocytotic cups, on the cell surface. We tested our method on both real and synthetic 3D image volumes, demonstrating that the inclusion of the curvature enhancement term can improve the segmentation of the aforementioned features. We show that our method performs better than other state of the art segmentation methods in 3D images of Dictyostelium cells, and performs competitively against CNN-based methods in two Cell Tracking Challenge datasets, demonstrating the ability to obtain accurate segmentations without the requirement of large training datasets. We also present an automated seeding method for microscopy data, which, combined with the curvature-enhanced random walker method, enables the segmentation of large time series with minimal input from the experimenter.

The Accumulation of Tau-Immunoreactive Hippocampal Granules and Corpora Amylacea Implicates Reactive Glia in Tau Pathogenesis during Aging.

SummaryThe microtubule-associated tau protein forms pathological inclusions that accumulate in an age-dependent manner in tauopathies including Alzheimer's disease (AD). Since age is the major risk factor for AD, we examined endogenous tau species that evolve during aging in physiological and diseased conditions. In aged mouse brain, we found tau-immunoreactive clusters embedded within structures that are reminiscent of periodic acid-Schiff (PAS) granules. We showed that PAS granules harbor distinct tau species that are more prominent in 3xTg-AD mice. Epitope profiling revealed hypo-phosphorylated rather than hyper-phosphorylated tau commonly observed in tauopathies. High-resolution imaging and 3D reconstruction suggest a link between tau clusters, reactive astrocytes, and microglia, indicating that early tau accumulation may promote neuroinflammation during aging. Using postmortem human brain, we identified tau as a component of corpora amylacea (CA), age-related structures that are functionally analogous to PAS granules. Overall, our study supports neuroimmune dysfunction as a precipitating event in tau pathogenesis.

Nan-O-Style – experiments and arts

In this project, high school students (aged 16-17) tested various protocols of experiments in nanotechnology and evaluated them whether such experiments could also be performed by middle school students (aged 11-15) or even elementary school students (aged 6-10). Protocols pre-selected and provided by the instructing team consisting of Sciencetainment and the Department of Biosciences, University of Salzburg were applied. Laboratory techniques such as thin-layer chromatography, measuring the contact angle by high-resolution 3D microscopy and analyzing and constructing surface layers represented some of the experiments performed. Moreover, students produced short video clips and images and designed photo-collages out of microscopic and electron microscopic pictures. Hence, the school students acquired a number of soft skills during this special science day.

Wide-field high-resolution 3D microscopy with Fourier ptychographic diffraction tomography

We report a computational 3D microscopy technique, termed Fourier ptychographic diffraction tomography (FPDT), that iteratively stitches together numerous variably illuminated, low-resolution images acquired with a low-numerical aperture (NA) objective in 3D Fourier space to create a wide field-of-view (FOV), high-resolution, depth-resolved complex refractive index (RI) image across large volumes. Unlike conventional optical diffraction tomography (ODT) approaches that rely on controlled bright-field illumination, holographic phase measurement, and high-NA objective detection, FPDT employs tomographic RI reconstruction from low-NA intensity-only measurements. In addition, FPDT incorporates high-angle dark-field illuminations beyond the NA of the objective, significantly expanding the accessible object frequency. With FPDT, we present the highest-throughput ODT results with 390 nm lateral resolution and 899 nm axial resolution across a 10 × FOV of 1.77 mm2 and a depth of focus of ~ 20 µm. Billion-voxel 3D tomographic imaging results of biological samples establish FPDT as a powerful non-invasive and label-free tool for high-throughput 3D microscopy applications.

Visualizing Adhesion Formation in Cells by Means of Advanced Spinning Disk-Total Internal Reflection Fluorescence Microscopy.

In living cells, processes such as adhesion formation involve extensive structural changes in the plasma membrane and the cell interior. In order to visualize these highly dynamic events, two complementary light microscopy techniques that allow fast imaging of live samples were combined: spinning disk microscopy (SD) for fast and high-resolution volume recording and total internal reflection fluorescence (TIRF) microscopy for precise localization and visualization of the plasma membrane. A comprehensive and complete imaging protocol will be shown for guiding through sample preparation, microscope calibration, image formation and acquisition, resulting in multi-color SD-TIRF live imaging series with high spatio-temporal resolution. All necessary image post-processing steps to generate multi-dimensional live imaging datasets, i.e. registration and combination of the individual channels, are provided in a self-written macro for the open source software ImageJ. The imaging of fluorescent proteins during initiation and maturation of adhesion complexes, as well as the formation of the actin cytoskeletal network, was used as a proof of principle for this novel approach. The combination of high resolution 3D microscopy and TIRF provided a detailed description of these complex processes within the cellular environment and, at the same time, precise localization of the membrane-associated molecules detected with a high signal-to-background ratio.

PiezoGRIN: A High-Pressure Chamber Incorporating GRIN Lenses for High-Resolution 3D-Microscopy of living Cells and Tissues.

A high‐pressure optical chamber, PiezoGRIN, that facilitates label‐free 3D high‐resolution live‐cell multiphoton microscopy in thick tissue samples is presented. A set of two Gradient Index (GRIN) rod lenses is integrated into the chamber as an optical guide and allows for the adjustment of the focal plane through the sample providing a field of view volume of 450 × 450 × 500 µm (x, y, z). An optical lateral resolution of 0.8 µm is achieved by using two‐photon excitation with 150 fs pulses of a 810 nm titanium–sapphire laser at hydrostatic pressures up to 200 MPa. With the PiezoGRIN setup, it is possible to follow pressure‐induced changes in subcellular structure of unstained vital mouse skeletal muscle tissue up to 200 µm below the tissue surface.

Interactive Visualization of 3D Histopathology in Native Resolution.

We present a visualization application that enables effective interactive visual analysis of large-scale 3D histopathology, that is, high-resolution 3D microscopy data of human tissue. Clinical work flows and research based on pathology have, until now, largely been dominated by 2D imaging. As we will show in the paper, studying volumetric histology data will open up novel and useful opportunities for both research and clinical practice. Our starting point is the current lack of appropriate visualization tools in histopathology, which has been a limiting factor in the uptake of digital pathology. Visualization of 3D histology data does pose difficult challenges in several aspects. The full-color datasets are dense and large in scale, on the order of 100,000 × 100,000× 100 voxels. This entails serious demands on both rendering performance and user experience design. Despite this, our developed application supports interactive study of 3D histology datasets at native resolution. Our application is based on tailoring and tuning of existing methods, system integration work, as well as a careful study of domain specific demands emanating from a close participatory design process with domain experts as team members. Results from a user evaluation employing the tool demonstrate a strong agreement among the 14 participating pathologists that 3D histopathology will be a valuable and enabling tool for their work.

High resolution 3D microscopy study of cardiomyocytes on polymer scaffold nanofibers reveals formation of unusual sheathed structure

Building functional and robust scaffolds for engineered biological tissue requires a nanoscale mechanistic understanding of how cells use the scaffold for their growth and development. A vast majority of the scaffolds used for cardiac tissue engineering are based on polymer materials, the matrices of nanofibers. Attempts to load the polymer fibers of the scaffold with additional sophisticated features, such as electrical conductivity and controlled release of the growth factors or other biologically active molecules, as well as trying to match the mechanical features of the scaffold to those of the extracellular matrix, cannot be efficient without a detailed knowledge of how the cells are attached and strategically positioned with respect to the scaffold nanofibers at micro and nanolevel. Studying single cell – single fiber interactions with the aid of confocal laser scanning microscopy (CLSM), scanning probe nanotomography (SPNT), and transmission electron microscopy (TEM), we found that cardiac cells actively interact with substrate nanofibers, but in different ways. While cardiomyocytes often create a remarkable “sheath” structure, enveloping fiber and, thus, substantially increasing contact zone, fibroblasts interact with nanofibers in the locations of focal adhesion clusters mainly without wrapping the fiber. Statements of SignificanceWe found that cardiomyocytes grown on electrospun polymer nanofibers often create a striking “sheath” structure, enveloping fiber with the formation of a very narrow (∼22 nm) membrane gap leading from the fiber to the extracellular space. This wrapping makes the entire fiber surface available for cell attachment. This finding gives a new prospective view on how scaffold nanofibers may interact with growing cells. It may play a significant role in effective design of novel nanofiber scaffolds for tissue engineering concerning mechanical and electrical properties of scaffolds as well as controlled drug release from “smart” biomaterials.

Fast submicrometer-scale imaging of whole zebrafish using the knife-edge scanning microscope.

Advances in high-resolution 3D microscopy have enabled the investigation of subcellular microstructures in biological specimen. For a full understanding of the organism's structure and function, it is mandatory to obtain data from the whole animal, not just parts of it. In this paper, we present our work with the Knife-Edge Scanning Microscope (KESM) for imaging a Nissl-stained whole zebrafish larva. KESM combines a diamond microtome and line-scan imaging for simultaneous sectioning and imaging in 3D. We show that using the KESM, a zebrafish, less than 3 mm long and diameter less than 500 μm, can be imaged within 1 hour at a resolution of 0.6 μm × 0.7 μm × 1.0 μm. We also present new results on using a vibrating microtome to improve sectioning and imaging robustness.

Toward Routine Use of 3D Histopathology as a Research Tool

Three-dimensional (3D) reconstruction and examination of tissue at microscopic resolution have significant potential to enhance the study of both normal and disease processes, particularly those involving structural changes or those in which the spatial relationship of disease features is important. Although other methods exist for studying tissue in 3D, using conventional histopathological features has significant advantages because it allows for conventional histopathological staining and interpretation techniques. Until now, its use has not been routine in research because of the technical difficulty in constructing 3D tissue models. We describe a novel system for 3D histological reconstruction, integrating whole-slide imaging (virtual slides), image serving, registration, and visualization into one user-friendly package. It produces high-resolution 3D reconstructions with minimal user interaction and can be used in a histopathological laboratory without input from computing specialists. It uses a novel method for slice-to-slice image registration using automatic registration algorithms custom designed for both virtual slides and histopathological images. This system has been applied to >300 separate 3D volumes from eight different tissue types, using a total of 5500 virtual slides comprising 1.45 TB of primary image data. Qualitative and quantitative metrics for the accuracy of 3D reconstruction are provided, with measured registration accuracy approaching 120 μm for a 1-cm piece of tissue. Both 3D tissue volumes and generated 3D models are presented for four demonstrator cases.

Multiscale Exploration of Mouse Brain Microstructures Using the Knife-Edge Scanning Microscope Brain Atlas

Connectomics is the study of the full connection matrix of the brain. Recent advances in high-throughput, high-resolution 3D microscopy methods have enabled the imaging of whole small animal brains at a sub-micrometer resolution, potentially opening the road to full-blown connectomics research. One of the first such instruments to achieve whole-brain-scale imaging at sub-micrometer resolution is the Knife-Edge Scanning Microscope (KESM). KESM whole-brain data sets now include Golgi (neuronal circuits), Nissl (soma distribution), and India ink (vascular networks). KESM data can contribute greatly to connectomics research, since they fill the gap between lower resolution, large volume imaging methods (such as diffusion MRI) and higher resolution, small volume methods (e.g., serial sectioning electron microscopy). Furthermore, KESM data are by their nature multiscale, ranging from the subcellular to the whole organ scale. Due to this, visualization alone is a huge challenge, before we even start worrying about quantitative connectivity analysis. To solve this issue, we developed a web-based neuroinformatics framework for efficient visualization and analysis of the multiscale KESM data sets. In this paper, we will first provide an overview of KESM, then discuss in detail the KESM data sets and the web-based neuroinformatics framework, which is called the KESM brain atlas (KESMBA). Finally, we will discuss the relevance of the KESMBA to connectomics research, and identify challenges and future directions.

Knife-Edge Scanning Microscope Brain Atlas: A Web-Based, Light-Weight 3D Mouse Brain Atlas

Event Abstract Back to Event Knife-Edge Scanning Microscope Brain Atlas: A Web-Based, Light-Weight 3D Mouse Brain Atlas Chul Sung1*, Ji Ryang Chung1, David Mayerich2, Jaerock Kwon3, Daniel Miller1, Todd Huffman4, John Keyser1, Louise Abbott1 and Yoonsuck Choe1 1 Texas A&M University, United States 2 University of Illinois, United States 3 Kettering University, United States 4 3Scan, United States High-throughput, high-resolution 3D microscopy techniques such as the Knife-Edge Scanning Microscopy (KESM) are enabling the acquisition of whole-brain-scale data from small animals such as the mouse. Using the fully automated KESM, we have been able to obtain whole mouse brain data sets at a resolution of 0.6 um x 0.7 um x 1.0 um, enough to show detailed neuronal morphology across the entire brain. Staining for our data sets were done with Golgi (neuronal morphology), Nissl (soma distribution), and India ink (vascular network). In this abstract, we describe a novel web-based 3D atlas we developed to enable broader access to our KESM data sets. The atlas framework, named the Knife-Edge Scanning Microscope Brain Atlas (KESMBA), customizes and extends the Google Maps API to serve the nearly 2TB (per brain) volume data in a multiscale manner, combined with a novel 3D rendering method using image overlays. The standard Google Maps navigation features (pan, zoom, etc.) are supported by default, allowing a multiscale exploration. Individual images in the data sets represent 1um-thin sections, so by themselves, they are not informative. We extended the Google Maps API to overcome this limitation, by overlaying images so that a local 3D volume can be visualized within the browser (see the figure). Other features include scale bar, navigation in the z (depth) direction, overlay control (number of overlays and interval), and location indicator. Experimental features include 3 standard sectioning planes (to be fully supported in the near future). KESMBA requires minimal client-side computing capability (a generic browser with javascript support), thus it enables broader dissemination of the KESM data sets to the neuroscience community. Also, we expect our framework to be general enough to accommodate other data modalities that have large volumes and fine details. On-going and future works include registration of the KESM data sets to the Waxholm space, and custom download and annotation functions. Acknowledgments: NSF CRCNS #0905041, NIH/NINDS \#1R01-NS54252, NSF MRI \#0079874, NSF ITR \#CCR-0220047, Texas ATP\#000512-0146-2001, Texas A\&M Research Foundation, Texas Engineering Experiment Station, and 3Scan. The appearance of the Google logo in the figure is due to the use of the Google Maps API by the KESM Brain Atlas. Besides that this work was done independent of Google. Figure 1 Keywords: digital atlasing, Neuroimaging Conference: 4th INCF Congress of Neuroinformatics, Boston, United States, 4 Sep - 6 Sep, 2011. Presentation Type: Poster Presentation Topic: Digital atlasing Citation: Sung C, Chung J, Mayerich D, Kwon J, Miller D, Huffman T, Keyser J, Abbott L and Choe Y (2011). Knife-Edge Scanning Microscope Brain Atlas: A Web-Based, Light-Weight 3D Mouse Brain Atlas. Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2011.08.00036 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 17 Oct 2011; Published Online: 19 Oct 2011. * Correspondence: Dr. Chul Sung, Texas A&M University, College Station, United States, csung@tamu.edu Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Chul Sung Ji Ryang Chung David Mayerich Jaerock Kwon Daniel Miller Todd Huffman John Keyser Louise Abbott Yoonsuck Choe Google Chul Sung Ji Ryang Chung David Mayerich Jaerock Kwon Daniel Miller Todd Huffman John Keyser Louise Abbott Yoonsuck Choe Google Scholar Chul Sung Ji Ryang Chung David Mayerich Jaerock Kwon Daniel Miller Todd Huffman John Keyser Louise Abbott Yoonsuck Choe PubMed Chul Sung Ji Ryang Chung David Mayerich Jaerock Kwon Daniel Miller Todd Huffman John Keyser Louise Abbott Yoonsuck Choe Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.