Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protocol for hybrid structured-light three-dimensional scanning and modeling of human postmortem brains.

ABSTRACT: Despite numerous neuropathological criteria for the evaluation of microscopic tissue slides, there are no systemic standards for sectioning postmortem human brain tissue. Here, we present a protocol for postmortem brain hybrid structured-light scanning to facilitate 3D printing of sectioning matrices. We describe steps for tissue preparation, 3D scanning and printing, and matrix-guided sectioning. This protocol can be used for streamlining tissue histopathology as well as in brain morphology volumetric analyses and applications in medical education. For complete details on the use and execution of this protocol, please refer to Barannikov et al.¹.

SUBMITTER: Smith MM

PROVIDER: S-EPMC11367453 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Protocol for hybrid structured-light three-dimensional scanning and modeling of human postmortem brains.

Smith Morgan Mekale MM Ochoa Elizabeth E Barannikov Savannah S Keating Mallory M Habes Mohamad M Flanagan Margaret E ME Seshadri Sudha S Bieniek Kevin F KF

STAR protocols 20240814 3

Despite numerous neuropathological criteria for the evaluation of microscopic tissue slides, there are no systemic standards for sectioning postmortem human brain tissue. Here, we present a protocol for postmortem brain hybrid structured-light scanning to facilitate 3D printing of sectioning matrices. We describe steps for tissue preparation, 3D scanning and printing, and matrix-guided sectioning. This protocol can be used for streamlining tissue histopathology as well as in brain morphology vol ...[more]

PMID: 39150849

Similar Datasets

Development of Three-Dimensional Dental Scanning Apparatus Using Structured Illumination.

Project description:We demonstrated a three-dimensional (3D) dental scanning apparatus based on structured illumination. A liquid lens was used for tuning focus and a piezomotor stage was used for the shift of structured light. A simple algorithm, which detects intensity modulation, was used to perform optical sectioning with structured illumination. We reconstructed a 3D point cloud, which represents the 3D coordinates of the digitized surface of a dental gypsum cast by piling up sectioned images. We performed 3D registration of an individual 3D point cloud, which includes alignment and merging the 3D point clouds to exhibit a 3D model of the dental cast.

| S-EPMC5539490 | biostudies-literature

A comparative study between traditional head measurement and structured light three-dimensional scanning when measuring infant head shape.

Project description:BackgroundThis study aimed to evaluate the correlation and consistency between traditional head measurement and structured light three-dimensional (3D) scanning parameters when measuring infant skull shape.MethodsA total of 76 infants aged 3 months to 2.5 years old were included in the study. Head circumference (HC) was measured with a tape measure. The transverse, anteroposterior, and oblique diameters were measured using a spreading caliper, and the cranial vault asymmetry index (CVAI) and a cranial index (CI) of symmetry were calculated; 76 cases were measured successfully. The above indexes were measured using a structured light 3D scanning system (71 cases were measured with success). Thus, in the end, the valid data of 71 cases were analyzed, and the measurements of the two approaches were compared.ResultsThe 95% confidence interval of traditional head measurement and structured light 3D scanning was between 0.633 and 0.988. Pearson's correlation coefficient indicated a high correlation between the two methods (r=0.793-0.980). The correlation coefficients of the transverse diameter, anteroposterior diameter, and HC, and the CI of symmetry were higher than 0.9. The lowest correlation coefficient for the CVAI was 0.793. The P values of the above measurement data were all <0.001, which indicated that they were closely related. A Bland-Altman plot indicated reasonable consistency between the two methods.ConclusionsBoth traditional head measurement and structured light 3D scanning are suitable for the measurement of infant head shape. However, while traditional head measurement using a spreading caliper is economical and simple, making it suitable for general screening at a basic level, structured light 3D scanning can deliver additional parameters, which is useful for infants with an abnormal head shape. The latter is also convenient for designing a customized helmet for skull correction when needed.

| S-EPMC8649591 | biostudies-literature

Metasurface-driven full-space structured light for three-dimensional imaging.

Project description:Structured light (SL)-based depth-sensing technology illuminates the objects with an array of dots, and backscattered light is monitored to extract three-dimensional information. Conventionally, diffractive optical elements have been used to form laser dot array, however, the field-of-view (FOV) and diffraction efficiency are limited due to their micron-scale pixel size. Here, we propose a metasurface-enhanced SL-based depth-sensing platform that scatters high-density ~10 K dot array over the 180° FOV by manipulating light at subwavelength-scale. As a proof-of-concept, we place face masks one on the beam axis and the other 50° apart from axis within distance of 1 m and estimate the depth information using a stereo matching algorithm. Furthermore, we demonstrate the replication of the metasurface using the nanoparticle-embedded-resin (nano-PER) imprinting method which enables high-throughput manufacturing of the metasurfaces on any arbitrary substrates. Such a full-space diffractive metasurface may afford ultra-compact depth perception platform for face recognition and automotive robot vision applications.

| S-EPMC9550774 | biostudies-literature

Three-dimensional scanning transmission electron microscopy of biological specimens.

Project description:A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2-3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset.

| S-EPMC2917646 | biostudies-literature

Adaptive optics in single objective inclined light sheet microscopy enables three-dimensional localization microscopy in adult <i>Drosophila</i> brains.

Project description:Single-molecule localization microscopy (SMLM) enables the high-resolution visualization of organelle structures and the precise localization of individual proteins. However, the expected resolution is not achieved in tissue as the imaging conditions deteriorate. Sample-induced aberrations distort the point spread function (PSF), and high background fluorescence decreases the localization precision. Here, we synergistically combine sensorless adaptive optics (AO), in-situ 3D-PSF calibration, and a single-objective lens inclined light sheet microscope (SOLEIL), termed (AO-SOLEIL), to mitigate deep tissue-induced deteriorations. We apply AO-SOLEIL on several dSTORM samples including brains of adult Drosophila. We observed a 2x improvement in the estimated axial localization precision with respect to widefield without aberration correction while we used synergistic solution. AO-SOLEIL enhances the overall imaging resolution and further facilitates the visualization of sub-cellular structures in tissue.

| S-EPMC9583434 | biostudies-literature

Three-dimensional structured illumination microscopy with enhanced axial resolution.

Project description:The axial resolution of three-dimensional structured illumination microscopy (3D SIM) is limited to ∼300 nm. Here we present two distinct, complementary methods to improve axial resolution in 3D SIM with minimal or no modification to the optical system. We show that placing a mirror directly opposite the sample enables four-beam interference with higher spatial frequency content than 3D SIM illumination, offering near-isotropic imaging with ∼120-nm lateral and 160-nm axial resolution. We also developed a deep learning method achieving ∼120-nm isotropic resolution. This method can be combined with denoising to facilitate volumetric imaging spanning dozens of timepoints. We demonstrate the potential of these advances by imaging a variety of cellular samples, delineating the nanoscale distribution of vimentin and microtubule filaments, observing the relative positions of caveolar coat proteins and lysosomal markers and visualizing cytoskeletal dynamics within T cells in the early stages of immune synapse formation.

| S-EPMC10497409 | biostudies-literature

Gene expression alterations in bipolar disorder postmortem brains.

Project description:? Bipolar disorder (BD) is a mental illness of unknown neuropathology and has several genetic associations. Antipsychotics are effective for the treatment of acute mania, psychosis, or mixed states in individuals with BD. We aimed to identify gene transcripts differentially expressed in postmortem brains from antipsychotics-exposed individuals with BD (hereafter the 'exposed' group), non-exposed individuals with BD (hereafter the 'non-exposed' group), and controls.? We quantified the abundance of gene transcripts in postmortem brains from seven exposed individuals, seven non-exposed individuals, and 12 controls with the Affymetrix U133P2 GeneChip microarrays and technologies. We applied a q-value of ?0.005 to identify statistically significant transcripts with mean abundance differences between the exposed, non-exposed and control groups.? We identified 2191 unique genes with significantly altered expression levels in non-exposed brains compared to those in the control and exposed groups. The expression levels of these genes were not significantly different between exposed brains and controls, suggesting a normalization effect of antipsychotics on the expression of these genes. Gene ontology (GO) enrichment analysis showed significant (Bonferroni p???0.05) clustering of subgroups of the 2191 genes under many GO terms; notably, the protein products of genes enriched are critical to the function of synapses, affecting, for example, intracellular trafficking and synaptic vesicle biogenesis, transport, release and recycling, as well as organization and stabilization of the node of Ranvier.? These results support a hypothesis of synaptic and intercellular communication impairment in BD. The apparent normalization of expression patterns with exposure to antipsychotic medication may represent a physiological process that relates both to etiology and improvement patterns of the disorder.

| S-EPMC3582727 | biostudies-other

The current progress and critical analysis of three-dimensional scanning and three-dimensional printing applications in breast surgery.

Project description:Several attempts have been made to develop a tool capable of evaluating breast shape and volume to aid surgical planning and outcome assessment. More recently, newer technologies such as three-dimensional (3D) scanning and 3D printing have been applied in breast assessment. The aim of this study was to review the literature to assess the applicability of 3D scanning and 3D printing in breast surgery. A literature search was carried on PubMed, Google Scholar and OVID from January 2000 to December 2019 using the keywords '3D', 'Three-dimensional', 'Three/four dimensions' and 'Breast'. A total of 6564 articles were identified initially; the abstracts of 1846 articles were scanned, and 81 articles met the inclusion criteria and were included in this review. Articles were reviewed and classified according to their aims, study subjects, the software and hardware used, main outcomes and major limitations. These technologies are fast and easy to use, however, high costs, long processing times and the need for training might limit their application. To incorporate these technologies into standard healthcare, their efficacy and effectiveness must be demonstrated through multiple and rigorous clinical trials.

| S-EPMC8105620 | biostudies-literature

Fast reconstruction and optical-sectioning three-dimensional structured illumination microscopy.

Project description:Three-dimensional structured illumination microscopy (3DSIM) is a popular method for observing subcellular/cellular structures or animal/plant tissues with gentle phototoxicity and 3D super-resolution. However, its time-consuming reconstruction process poses challenges for high-throughput imaging and real-time observation. Moreover, traditional 3DSIM typically requires more than six z layers for successful reconstruction and is susceptible to defocused backgrounds. This poses a great gap between single-layer 2DSIM and 6-layer 3DSIM, and limits the observation of thicker samples. To address these limitations, we developed FO-3DSIM, a novel method that integrates spatial-domain reconstruction with optical-sectioning SIM. FO-3DSIM enhances reconstruction speed by up to 855.7 times with superior performance with limited z layers and under high defocused backgrounds. It retains the high-fidelity, low-photon reconstruction capabilities of our previously proposed Open-3DSIM. Utilizing fast reconstruction and optical sectioning, we achieved large field-of-view (FOV) 3D super-resolution imaging of mouse kidney actin, covering a region of 0.453 mm × 0.453 mm × 2.75 μm within 23 min of acquisition and 13 min of reconstruction. Near real-time performance was demonstrated in live actin imaging with FO-3DSIM. Our approach reduces photodamage through limited z layer reconstruction, allowing the observation of ER tubes with just three layers. We anticipate that FO-3DSIM will pave the way for near real-time, large FOV 6D imaging, encompassing xyz super-resolution, multi-color, long-term, and polarization imaging with less photodamage, removed defocused backgrounds, and reduced reconstruction time.

| S-EPMC11846033 | biostudies-literature

Structured-light surface scanning system to evaluate breast morphology in standing and supine positions.

Project description:Breast shapes are affected by gravitational loads and deformities. Measurements obtained in the standing position may not correlate well with measurements in the supine position, which is more representative of patient position during breast surgery. A dual color 3D surface imaging system capable of scanning patients in both supine and standing positions was developed to evaluate the effect of changes in body posture on breast morphology. The system was evaluated with breast phantoms to assess accuracy, then tested on ten subjects in three body postures to assess its effectiveness as a clinical tool. The accuracy of the system was within 0.4 mm on average across the model. For the human study, there was no effect of body posture on breast volumes (p value > 0.05), but we observed an effect of completeness of breast scans on body posture (p value < 0.05). Post-hoc tests showed that the supine position and the standing position with hands at the waist differed significantly (p value < 0.05). This study shows that the system can quantitatively evaluate the effect of subject postures, and thereby has the potential to be used to investigate peri-operative changes in breast morphology.

| S-EPMC7445296 | 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