Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

3DSEM: A 3D microscopy dataset.

ABSTRACT: The Scanning Electron Microscope (SEM) as a 2D imaging instrument has been widely used in many scientific disciplines including biological, mechanical, and materials sciences to determine the surface attributes of microscopic objects. However the SEM micrographs still remain 2D images. To effectively measure and visualize the surface properties, we need to truly restore the 3D shape model from 2D SEM images. Having 3D surfaces would provide anatomic shape of micro-samples which allows for quantitative measurements and informative visualization of the specimens being investigated. The 3DSEM is a dataset for 3D microscopy vision which is freely available at [1] for any academic, educational, and research purposes. The dataset includes both 2D images and 3D reconstructed surfaces of several real microscopic samples.

SUBMITTER: Tafti AP

PROVIDER: S-EPMC4685174 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

3DSEM: A 3D microscopy dataset.

Tafti Ahmad P AP Kirkpatrick Andrew B AB Holz Jessica D JD Owen Heather A HA Yu Zeyun Z

Data in brief 20151202

The Scanning Electron Microscope (SEM) as a 2D imaging instrument has been widely used in many scientific disciplines including biological, mechanical, and materials sciences to determine the surface attributes of microscopic objects. However the SEM micrographs still remain 2D images. To effectively measure and visualize the surface properties, we need to truly restore the 3D shape model from 2D SEM images. Having 3D surfaces would provide anatomic shape of micro-samples which allows for quanti ...[more]

PMID: 26779561

Similar Datasets

A 3D Brillouin microscopy dataset of the in-vivo zebrafish eye.

Project description:In this work we present three-dimensional (3D) measurements of Brillouin scattering spectra of the in-vivo zebrafish larvae eye. This dataset was obtained by Brillouin microscopy, an emerging all-optical and non-contact technique that gives access to material properties through the process of Brillouin scattering. Herein, we share a representative 3D dataset of spectral properties of 48-52 h post-fertilization (hpf) zebrafish embryos. These spectral properties can be related to a complex longitudinal modulus and thus elastic and viscous properties given knowledge of refractive index and material density. The dataset encompasses the crystalline lens as well as several different retinal layers. This data provides a valuable resource as well as a starting point for researchers interested in the mechanobiology of vertebrate eye development.

| S-EPMC7132165 | biostudies-literature

Cell lines and clearing approaches: a single-cell level 3D light-sheet fluorescence microscopy dataset of multicellular spheroids.

Project description:Nowadays, three dimensional (3D) cell cultures are widely used in the biological laboratories and several optical clearing approaches have been proposed to visualize individual cells in the deepest layers of cancer multicellular spheroids. However, defining the most appropriate clearing approach for the different cell lines is an open issue due to the lack of a gold standard quantitative metric. In this article, we describe and share a single-cell resolution 3D image dataset of human carcinoma spheroids imaged using a light-sheet fluorescence microscope. The dataset contains 90 multicellular cancer spheroids derived from 3 cell lines (i.e. T-47D, 5-8F, and Huh-7D12) and cleared with 5 different protocols, precisely ClearT, ClearT2, CUBIC, ScaleA2, and Sucrose. To evaluate image quality and light penetration depth of the cleared 3D samples, all the spheroids have been imaged under the same experimental conditions, labelling the nuclei with the DRAQ5 stain and using a Leica SP8 Digital LightSheet microscope. The clearing quality of this dataset was annotated by 10 independent experts and thus allows microscopy users to qualitatively compare the effects of different optical clearing protocols on different cell lines. It is also an optimal testbed to quantitatively assess different computational metrics evaluating the image quality in the deepest layers of the spheroids.

| S-EPMC8134717 | biostudies-literature

3D Viscoelastic traction force microscopy.

Project description:Native cell-material interactions occur on materials differing in their structural composition, chemistry, and physical compliance. While the last two decades have shown the importance of traction forces during cell-material interactions, they have been almost exclusively presented on purely elastic in vitro materials. Yet, most bodily tissue materials exhibit some level of viscoelasticity, which could play an important role in how cells sense and transduce tractions. To expand the realm of cell traction measurements and to encompass all materials from elastic to viscoelastic, this paper presents a general, and comprehensive approach for quantifying 3D cell tractions in viscoelastic materials. This methodology includes the experimental characterization of the time-dependent material properties for any viscoelastic material with the subsequent mathematical implementation of the determined material model into a 3D traction force microscopy (3D TFM) framework. Utilizing this new 3D viscoelastic TFM (3D VTFM) approach, we quantify the influence of viscosity on the overall material traction calculations and quantify the error associated with omitting time-dependent material effects, as is the case for all other TFM formulations. We anticipate that the 3D VTFM technique will open up new avenues of cell-material investigations on even more physiologically relevant time-dependent materials including collagen and fibrin gels.

| S-EPMC4176508 | biostudies-literature

RAP3DF - One shoot 3D face dataset.

Project description:Develop researches in the 3D biometrics field requires a large set of images, whether for training the algorithms or during the recognition test. Several datasets can be found in the literature. In an analysis of these datasets it was observed that a single dataset does not have the types of infrared images, visible and three-dimensional light, for the same sample. Given this context, the present work conceived this 3D facial dataset, with its respective visible light image and infrared spectrum, providing the entire image acquisition process from the Kinect One device. The work consists of 267 samples from 64 volunteers, where each volunteer has a frontal facial image and 3 images in arbitrary positions.

| S-EPMC7509182 | biostudies-literature

CIVIT dataset: Integral microscopy with Fourier plane recording.

Project description:This article describes a dataset of synthetic images representing biological scenery as captured by a Fourier Lightfield Microscope (FLMic). It includes 22,416 images related to eight scenes composed of 3D models of objects typical for biological samples, such as red blood cells and bacteria, and categorized into Cells and Filaments groups. For each scene, two types of image data structures are provided: 51 × 51 Elemental Images (EIs) representing Densely Sampled Light Fields (DSLF) and 201 images composing Z-Scans of the scenes. Auxiliary data also includes information about camera intrinsic and extrinsic calibration parameters, object descriptions, and MATLAB scripts for camera pose compensation. The images have been generated using Blender. The dataset can be used to develop and assess methods for volumetric reconstruction from Light Field (LF) images captured by a FLMic.

| S-EPMC9801074 | biostudies-literature

Simple buffers for 3D STORM microscopy.

Project description:3D STORM is one of the leading methods for super-resolution imaging, with resolution down to 10 nm in the lateral direction, and 30-50 nm in the axial direction. However, there is one important requirement to perform this type of imaging: making dye molecules blink. This usually relies on the utilization of complex buffers, containing different chemicals and sensitive enzymatic systems, limiting the reproducibility of the method. We report here that the commercial mounting medium Vectashield can be used for STORM of Alexa-647, and yields images comparable or superior to those obtained with more complex buffers, especially for 3D imaging. We expect that this advance will promote the versatile utilization of 3D STORM by removing one of its entry barriers, as well as provide a more reproducible way to compare optical setups and data processing algorithms.

| S-EPMC3675867 | biostudies-literature

A 3D texture dataset of 27 km road.

Project description:This dataset represents the 3D road surface texture of a route of 27 km long in a resolution of 0.1 m approximatively in both longitudinal and transversal directions. The first purpose of the dataset is to test numerical programs that need road surface topographies as input. The dataset is composed of 2658 text files and each representing a section of that route. The data was collected with the Harris2, a vehicle operated by TRL (Transport Research Laboratory from the UK), equipped with a LiDAR (Light Detection and Ranging) and a PPS (Road-Profile System). The files are presented in a regular grid achieved by merging the LIDAR and the PPS data into 3D coordinates.

| S-EPMC7900215 | biostudies-literature

Lens-free microscopy for 3D + time acquisitions of 3D cell culture.

Project description:Thanks to a novel three-dimensional imaging platform based on lens-free microscopy, it is possible to perform multi-angle acquisitions and holographic reconstructions of 3D cell cultures directly into the incubator. Being able of reconstructing volumes as large as ~5?mm3 over a period of time covering several days, allows us to observe a broad range of migration strategies only present in 3D environment, whether it is single cell migration, collective migrations of cells and dispersal of cells. In addition we are able to distinguish new interesting phenomena, e.g. large-scale cell-to-matrix interactions (>1?mm), fusion of cell clusters into large aggregate (~10,000?µm2) and conversely, total dissociation of cell clusters into clumps of migrating cells. This work on a novel 3D?+?time lens-free microscopy technique thus expands the repertoire of phenomena that can be studied within 3D cell cultures.

| S-EPMC6208343 | biostudies-literature

ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range.

Project description:Single molecule localization microscopy can generate 3D super-resolution images without scanning by leveraging the axial variations of normal or engineered point spread functions (PSF). Successful implementation of these approaches for extended axial ranges remains, however, challenging. We present Zernike Optimized Localization Approach in 3D (ZOLA-3D), an easy-to-use computational and optical solution that achieves optimal resolution over a tunable axial range. We use ZOLA-3D to demonstrate 3D super-resolution imaging of mitochondria, nuclear pores and microtubules in entire nuclei or cells up to ~5??m deep.

| S-EPMC6008307 | biostudies-literature

Unmanned aerial image dataset: Ready for 3D reconstruction.

Project description:Unmanned aerial vehicles (UAVs) have become popular platforms for collecting various types of geospatial data for various mapping, monitoring and modelling applications. With the advancement of imaging and computing technologies, a vast variety of photogrammetric, computer-vision and, nowadays, end-to-end learning workflows are introduced to produce three-dimensional (3D) information in form of digital surface and terrain models, textured meshes, rectified mosaics, CAD models, etc. These 3D products might be used in applications where accuracy and precision play a vital role, e.g. structural health monitoring. Therefore, extensive tests against data with relevant characteristics and reliable ground-truth are required to assess and ensure the performance of 3D modelling workflows. This article describes the images collected by a customized unmanned aerial vehicle (UAV) system from an open-pit gravel mine accompanied with additional data that will allow implementing and evaluating any structure-from-motion or photogrammetric approach for sparse or dense 3D reconstruction. This dataset includes total of 158 high-quality images captured with more than 80% endlap and spatial resolution higher than 1.5 cm, the 3D coordinates of 109 ground control points and checkpoints, 2D coordinates of more than 40K corresponding points among the images, a subset of 25 multi-view stereo images selected from an area of approximately 30 m × 40 m within the scene accompanied with a dense point cloud measured by a terrestrial laser scanner.

| S-EPMC6554229 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data