Dataset Information

A proposal of a new automated method for SfM/MVS 3D reconstruction through comparisons of 3D data by SfM/MVS and handheld laser scanners.

ABSTRACT: SfM/MVS photogrammetry has received increasing attention due to its convenience, broadening the range of its applications into archaeology and anthropology. Because the accuracy of SfM/MVS depends on photography, one important issue is that incorrect or low-density point clouds are found in 3D models due to poor overlapping between images. A systematic way of taking photographs solve these problems, though it has not been well established and the accuracy has not been examined either, with some exceptions. The present study aims to (i) develop an efficient method for recording pottery using an automated turntable and (ii) assess its accuracy through a comparison with 3D models made by laser scanning. We recorded relatively simple pottery manufactured by prehistoric farmers in the Japanese archipelago using SfM/MVS photogrammetry and laser scanning. Further, by measuring the Hausdorff distance between 3D models made using these two methods, we show that their difference is negligibly small, suggesting that our method is sufficiently accurate to record pottery.

SUBMITTER: Kaneda A

PROVIDER: S-EPMC9299387 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A proposal of a new automated method for SfM/MVS 3D reconstruction through comparisons of 3D data by SfM/MVS and handheld laser scanners.

Kaneda Akihiro A Nakagawa Tomomi T Tamura Kohei K Noshita Koji K Nakao Hisashi H

PloS one 20220720 7

SfM/MVS photogrammetry has received increasing attention due to its convenience, broadening the range of its applications into archaeology and anthropology. Because the accuracy of SfM/MVS depends on photography, one important issue is that incorrect or low-density point clouds are found in 3D models due to poor overlapping between images. A systematic way of taking photographs solve these problems, though it has not been well established and the accuracy has not been examined either, with some ...[more]

PMID: 35857749

Similar Datasets

Project description:Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.

Project description:BackgroundCryo-EM data generated by electron tomography (ET) contains images for individual protein particles in different orientations and tilted angles. Individual cryo-EM particles can be aligned to reconstruct a 3D density map of a protein structure. However, low contrast and high noise in particle images make it challenging to build 3D density maps at intermediate to high resolution (1-3 Å). To overcome this problem, we propose a fully automated cryo-EM 3D density map reconstruction approach based on deep learning particle picking.ResultsA perfect 2D particle mask is fully automatically generated for every single particle. Then, it uses a computer vision image alignment algorithm (image registration) to fully automatically align the particle masks. It calculates the difference of the particle image orientation angles to align the original particle image. Finally, it reconstructs a localized 3D density map between every two single-particle images that have the largest number of corresponding features. The localized 3D density maps are then averaged to reconstruct a final 3D density map. The constructed 3D density map results illustrate the potential to determine the structures of the molecules using a few samples of good particles. Also, using the localized particle samples (with no background) to generate the localized 3D density maps can improve the process of the resolution evaluation in experimental maps of cryo-EM. Tested on two widely used datasets, Auto3DCryoMap is able to reconstruct good 3D density maps using only a few thousand protein particle images, which is much smaller than hundreds of thousands of particles required by the existing methods.ConclusionsWe design a fully automated approach for cryo-EM 3D density maps reconstruction (Auto3DCryoMap). Instead of increasing the signal-to-noise ratio by using 2D class averaging, our approach uses 2D particle masks to produce locally aligned particle images. Auto3DCryoMap is able to accurately align structural particle shapes. Also, it is able to construct a decent 3D density map from only a few thousand aligned particle images while the existing tools require hundreds of thousands of particle images. Finally, by using the pre-processed particle images, Auto3DCryoMap reconstructs a better 3D density map than using the original particle images.

Project description:Measurements of auditory ossicles displacement are commonly carried out by means of laser-Doppler vibrometry (LDV), which is considered to be a gold standard. The limitation of the LDV method, especially for in vivo measurements, is the necessity to expose an object in a straight line to a laser beam operating from a distance. An alternative to this approach is the use of a handheld laser-fiber vibrometry probe (HLFVP) with a curved tip. We evaluate the feasibility of an HLFVP with a curved tip for measuring sound-induced displacement of the auditory ossicles. A handheld vibrometer probe guiding the laser beam with a fiber-optic cable was used for displacement measurements of the incus body and the posterior crus of the stapes. Tonal stimuli at frequencies of 0.5, 1, 2, and 4 kHz were presented by means of an insert earphone positioned in the outer ear canal. The probe was fixed at the measurement site using a tripod or hand-held by one of the two surgeons. The measurements were carried out on six fresh temporal bones. Multivariate analysis of variance showed statistically significant differences for stimulus frequency (F3,143 = 29.37, p < 0.001, and η2 = 0.35), bone (F5,143 = 4.61, p = 0.001, and η2 = 0.01), and measurement site (F1,143 = 4.74, p = 0.03, and η2 = 0.02) in the absence of statistically significant differences for the probe fixation method (F2,143 = 0.15, p = 0.862, and η2 = 0.001). Standard deviations of the means were 6.9, 2.6, 1.9, and 0.6 nm / Pa for frequency, bone, site, and fixation, respectively. Ear transfer functions were found to be consistent with literature data. The feasibility of applying HLFVP to measure the displacement of auditory ossicles has been confirmed. HLFVP offers the possibility of carrying out measurements at various angles; however, this needs to be standardized taking into account anatomical limitations and surgical convenience.

Dataset Information

A proposal of a new automated method for SfM/MVS 3D reconstruction through comparisons of 3D data by SfM/MVS and handheld laser scanners.

Publications

A proposal of a new automated method for SfM/MVS 3D reconstruction through comparisons of 3D data by SfM/MVS and handheld laser scanners.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets