scholarly journals The Lightfield Microscope Eyepiece

Sensors ◽  
2021 ◽  
Vol 21 (19) ◽  
pp. 6619
Author(s):  
Nicolò Incardona ◽  
Ángel Tolosa ◽  
Gabriele Scrofani ◽  
Manuel Martinez-Corral ◽  
Genaro Saavedra
Keyword(s):  
3D Reconstruction ◽  
Time Resolution ◽  
Optical Design ◽  
Three Dimensional ◽  
Fourier Integral ◽  
Single Shot ◽  
Proof Of Concept ◽  
Novel Device ◽  
Translation Stage ◽  
Commercial Device

Lightfield microscopy has raised growing interest in the last few years. Its ability to get three-dimensional information about the sample in a single shot makes it suitable for many applications in which time resolution is fundamental. In this paper we present a novel device, which is capable of converting any conventional microscope into a lightfield microscope. Based on the Fourier integral microscope concept, we designed the lightfield microscope eyepiece. This is coupled to the eyepiece port, to let the user exploit all the host microscope’s components (objective turret, illumination systems, translation stage, etc.) and get a 3D reconstruction of the sample. After the optical design, a proof-of-concept device was built with off-the-shelf optomechanical components. Here, its optical performances are demonstrated, which show good matching with the theoretical ones. Then, the pictures of different samples taken with the lightfield eyepiece are shown, along with the corresponding reconstructions. We demonstrated the functioning of the lightfield eyepiece and lay the foundation for the development of a commercial device that works with any microscope.

scholarly journals Robust Depth Estimation for Light Field Microscopy

Sensors ◽  
2019 ◽  
Vol 19 (3) ◽  
pp. 500 ◽  
Author(s):  
Luca Palmieri ◽  
Gabriele Scrofani ◽  
Nicolò Incardona ◽  
Genaro Saavedra ◽  
Manuel Martínez-Corral ◽  
...  
Keyword(s):  
Light Field ◽  
Three Dimensional ◽  
Depth Map ◽  
Depth Estimation ◽  
Fourier Integral ◽  
Single Shot ◽  
Natural Scene ◽  
Multi Scale ◽  
Depth Maps ◽  
New Applications

Light field technologies have seen a rise in recent years and microscopy is a field where such technology has had a deep impact. The possibility to provide spatial and angular information at the same time and in a single shot brings several advantages and allows for new applications. A common goal in these applications is the calculation of a depth map to reconstruct the three-dimensional geometry of the scene. Many approaches are applicable, but most of them cannot achieve high accuracy because of the nature of such images: biological samples are usually poor in features and do not exhibit sharp colors like natural scene. Due to such conditions, standard approaches result in noisy depth maps. In this work, a robust approach is proposed where accurate depth maps can be produced exploiting the information recorded in the light field, in particular, images produced with Fourier integral Microscope. The proposed approach can be divided into three main parts. Initially, it creates two cost volumes using different focal cues, namely correspondences and defocus. Secondly, it applies filtering methods that exploit multi-scale and super-pixels cost aggregation to reduce noise and enhance the accuracy. Finally, it merges the two cost volumes and extracts a depth map through multi-label optimization.

Detection, Averaging, and 3D Reconstruction of Biological Specimens on Hypercubes (Transputer-based) Computers

1990 ◽  
Vol 48 (1) ◽  
pp. 454-455
Author(s):  
Jose-Maria Carazo ◽  
I. Benavides ◽  
S. Marco ◽  
J.L. Carrascosa ◽  
E.L. Zapata
Keyword(s):  
3D Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Software Tools ◽  
Mapping Method ◽  
Computer Architectures ◽  
Parallel Computer ◽  
Reconstruction Process ◽  
Computing Power ◽  
Order Of Magnitude

Obtaining the three-dimensional (3D) structure of negatively stained biological specimens at a resolution of, typically, 2 - 4 nm is becoming a relatively common practice in an increasing number of laboratories. A combination of new conceptual approaches, new software tools, and faster computers have made this situation possible. However, all these 3D reconstruction processes are quite computer intensive, and the middle term future is full of suggestions entailing an even greater need of computing power. Up to now all published 3D reconstructions in this field have been performed on conventional (sequential) computers, but it is a fact that new parallel computer architectures represent the potential of order-of-magnitude increases in computing power and should, therefore, be considered for their possible application in the most computing intensive tasks.We have studied both shared-memory-based computer architectures, like the BBN Butterfly, and local-memory-based architectures, mainly hypercubes implemented on transputers, where we have used the algorithmic mapping method proposed by Zapata el at. In this work we have developed the basic software tools needed to obtain a 3D reconstruction from non-crystalline specimens (“single particles”) using the so-called Random Conical Tilt Series Method. We start from a pair of images presenting the same field, first tilted (by ≃55°) and then untilted. It is then assumed that we can supply the system with the image of the particle we are looking for (ideally, a 2D average from a previous study) and with a matrix describing the geometrical relationships between the tilted and untilted fields (this step is now accomplished by interactively marking a few pairs of corresponding features in the two fields). From here on the 3D reconstruction process may be run automatically.

3D reconstruction and calculation of surface area and volume of bell pepper

2007 ◽  
Vol 3 (1) ◽  
pp. 89-113
Author(s):  
Zoltán Gillay ◽  
László Fenyvesi
Keyword(s):  
3D Reconstruction ◽  
Surface Area ◽  
Three Dimensional ◽  
Reference Method ◽  
Bell Pepper ◽  
Three Dimensional Model ◽  
Acceptable Error ◽  
Volume Calculation ◽  
Bell Peppers ◽  
Area And Volume

There was a method developed that generates the three-dimensional model of not axisymmetric produce, based on an arbitrary number of photos. The model can serve as a basis for calculating the surface area and the volume of produce. The efficiency of the reconstruction was tested on bell peppers and artificial shapes. In case of bell peppers 3-dimensional reconstruction was created from 4 images rotated in 45° angle intervals. The surface area and the volume were estimated on the basis of the reconstructed area. Furthermore, a new and simple reference method was devised to give precise results for the surface area of bell pepper. The results show that this 3D reconstruction-based surface area and volume calculation method is suitable to determine the surface area and volume of definite bell peppers with an acceptable error.

Three-dimensional Reconstruction of Microscopic Image Based on Multi-ST Algorithm

2020 ◽  
Vol 64 (2) ◽  
pp. 20506-1-20506-7
Author(s):  
Min Zhu ◽  
Rongfu Zhang ◽  
Pei Ma ◽  
Xuedian Zhang ◽  
Qi Guo
Keyword(s):  
3D Reconstruction ◽  
Three Dimensional ◽  
Scale Model ◽  
Microscopic Image ◽  
Multi Scale ◽  
Gaussian Pyramid ◽  
Cost Aggregation ◽  
Dimensional Reconstruction ◽  
Image Pairs ◽  
Accurate Matching

Abstract Three-dimensional (3D) reconstruction is extensively used in microscopic applications. Reducing excessive error points and achieving accurate matching of weak texture regions have been the classical challenges for 3D microscopic vision. A Multi-ST algorithm was proposed to improve matching accuracy. The process is performed in two main stages: scaled microscopic images and regularized cost aggregation. First, microscopic image pairs with different scales were extracted according to the Gaussian pyramid criterion. Second, a novel cost aggregation approach based on the regularized multi-scale model was implemented into all scales to obtain the final cost. To evaluate the performances of the proposed Multi-ST algorithm and compare different algorithms, seven groups of images from the Middlebury dataset and four groups of experimental images obtained by a binocular microscopic system were analyzed. Disparity maps and reconstruction maps generated by the proposed approach contained more information and fewer outliers or artifacts. Furthermore, 3D reconstruction of the plug gauges using the Multi-ST algorithm showed that the error was less than 0.025 mm.

scholarly journals A 3D hydrodynamic flow-focusing device for cell sorting

2021 ◽  
Vol 25 (3) ◽  
Author(s):  
Xiaofei Yuan ◽  
Andrew Glidle ◽  
Hitoshi Furusho ◽  
Huabing Yin
Keyword(s):  
Cell Sorting ◽  
Control Strategies ◽  
Three Dimensional ◽  
Hydrodynamic Flow ◽  
Proof Of Concept ◽  
Flow Focusing ◽  
Hydrodynamic Focusing ◽  
Cell Handling ◽  
Fluid Flow Control ◽  
High Degree

AbstractOptical-based microfluidic cell sorting has become increasingly attractive for applications in life and environmental sciences due to its ability of sophisticated cell handling in flow. The majority of these microfluidic cell sorting devices employ two-dimensional fluid flow control strategies, which lack the ability to manipulate the position of cells arbitrarily for precise optical detection, therefore resulting in reduced sorting accuracy and purity. Although three-dimensional (3D) hydrodynamic devices have better flow-focusing characteristics, most lack the flexibility to arbitrarily position the sample flow in each direction. Thus, there have been very few studies using 3D hydrodynamic flow focusing for sorting. Herein, we designed a 3D hydrodynamic focusing sorting platform based on independent sheath flow-focusing and pressure-actuated switching. This design offers many advantages in terms of reliable acquisition of weak Raman signals due to the ability to precisely control the speed and position of samples in 3D. With a proof-of-concept demonstration, we show this 3D hydrodynamic focusing-based sorting device has the potential to reach a high degree of accuracy for Raman activated sorting.

scholarly journals A Proof-of-Concept Algorithm for the Retrieval of Total Column Amount of Trace Gases in a Multi-Dimensional Atmosphere

2021 ◽  
Vol 13 (2) ◽  
pp. 270
Author(s):  
Adrian Doicu ◽  
Dmitry S. Efremenko ◽  
Thomas Trautmann
Keyword(s):  
Trace Gases ◽  
Three Dimensional ◽  
Principal Component ◽  
Radiative Transfer Model ◽  
Computational Time ◽  
Transfer Model ◽  
Proof Of Concept ◽  
Discrete Ordinate ◽  
Distribution Method ◽  
Total Column

An algorithm for the retrieval of total column amount of trace gases in a multi-dimensional atmosphere is designed. The algorithm uses (i) certain differential radiance models with internal and external closures as inversion models, (ii) the iteratively regularized Gauss–Newton method as a regularization tool, and (iii) the spherical harmonics discrete ordinate method (SHDOM) as linearized radiative transfer model. For efficiency reasons, SHDOM is equipped with a spectral acceleration approach that combines the correlated k-distribution method with the principal component analysis. The algorithm is used to retrieve the total column amount of nitrogen for two- and three-dimensional cloudy scenes. Although for three-dimensional geometries, the computational time is high, the main concepts of the algorithm are correct and the retrieval results are accurate.

scholarly journals 3D Reconstruction of Cultural Heritage Sites as an Educational Approach. The Sanctuary of Delphi

2021 ◽  
Vol 11 (8) ◽  
pp. 3635
Author(s):  
Ioannis Liritzis ◽  
Pantelis Volonakis ◽  
Spyros Vosinakis
Keyword(s):  
University Students ◽  
3D Reconstruction ◽  
Cultural Heritage ◽  
New Technology ◽  
Three Dimensional ◽  
Computer Gaming ◽  
Educational Approach ◽  
Heritage Sites ◽  
3D Environment ◽  
Almost All

In the field of cultural heritage, three-dimensional (3D) reconstruction of monuments is a usual activity for many professionals. The aim in this paper focuses on the new technology educational application combining science, history, and archaeology. Being involved in almost all stages of implementation steps and assessing the level of participation, university students use tools of computer gaming platform and participate in ways of planning the virtual environment which improves their education through e-Learning. The virtual 3D environment is made with different imaging methods (helium-filled balloon, Structure for motion, 3D repository models) and a developmental plan has been designed for use in many future applications. Digital tools were used with 3D reconstructed buildings from the museum archive to Unity 3D for the design. The pilot study of Information Technology work has been employed to introduce cultural heritage and archaeology to university syllabuses. It included students with a questionnaire which has been evaluated accordingly. As a result, the university students were inspired to immerse themselves into the virtual lab, aiming to increasing the level of interaction. The results show a satisfactory learning outcome by an easy to use and real 3D environment, a step forward to fill in needs of contemporary online sustainable learning demands.

scholarly journals 3D Reconstruction with Single-Shot Structured Light RGB Line Pattern

Sensors ◽  
2021 ◽  
Vol 21 (14) ◽  
pp. 4819
Author(s):  
Yikang Li ◽  
Zhenzhou Wang
Keyword(s):  
3D Reconstruction ◽  
Moving Objects ◽  
Structured Light ◽  
Color Space ◽  
Reconstruction Technique ◽  
Single Shot ◽  
Line Pattern ◽  
Hsv Color Space ◽  
Phase Map ◽  
Line Segmentation

Single-shot 3D reconstruction technique is very important for measuring moving and deforming objects. After many decades of study, a great number of interesting single-shot techniques have been proposed, yet the problem remains open. In this paper, a new approach is proposed to reconstruct deforming and moving objects with the structured light RGB line pattern. The structured light RGB line pattern is coded using parallel red, green, and blue lines with equal intervals to facilitate line segmentation and line indexing. A slope difference distribution (SDD)-based image segmentation method is proposed to segment the lines robustly in the HSV color space. A method of exclusion is proposed to index the red lines, the green lines, and the blue lines respectively and robustly. The indexed lines in different colors are fused to obtain a phase map for 3D depth calculation. The quantitative accuracies of measuring a calibration grid and a ball achieved by the proposed approach are 0.46 and 0.24 mm, respectively, which are significantly lower than those achieved by the compared state-of-the-art single-shot techniques.

scholarly journals Three-dimensional analysis of the root canal preparation with Reciproc Blue®, WaveOne Gold® and XP EndoShaper®: a new method in vivo

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Javier Caviedes-Bucheli ◽  
Nestor Rios-Osorio ◽  
Diana Usme ◽  
Cristian Jimenez ◽  
Adriana Pinzon ◽  
...  
Keyword(s):  
3D Reconstruction ◽  
Root Canal ◽  
Paired Comparison ◽  
Three Dimensional ◽  
New Method ◽  
Root Canal Preparation ◽  
Paired Data ◽  
Before And After ◽  
Student’S T

Abstract Background The purpose of this study was to evaluate the changes in canal volume after root canal preparation in vivo with 3 different single-file techniques (Reciproc-Blue®, WaveOne-Gold® and XP-EndoShaper®), with a new method using CBCT and 3D reconstruction. Methods In this prospective study, thirty human lower premolars from healthy patients were used, in which extraction was indicated for orthodontic reasons. All the teeth used were caries- and restoration-free with complete root development, without signs of periodontal disease or traumatic occlusion, and with only one straight canal (up to 25º curvature). Teeth were randomly divided into three different groups: Reciproc-Blue, WaveOne-Gold and XP-EndoShaper. CBCT scans before root canal preparation were used to create a 3D reconstruction with RHINOCEROS 5.0 software to assess the initial canal volume, and then compared with 3D reconstructions after canal preparation to measure the increase in canal volume. Student’s t test for paired data were used to determine statistically significant differences between the before and after canal volumes. Anova test was used to determine statistically significant differences in the percentage of canal volume increase between the groups and Tukey's post-hoc test were used to paired comparison. Results Reciproc-Blue showed the higher increase in canal volume, followed by WaveOne-Gold and XP-EndoShaper (p = 0.003). XP-EndoShaper did not show a statistically significant increase in canal volume after root canal preparation (p = 0.06). Conclusion With this model, Reciproc-Blue showed higher increase in root canal volume, followed by WaveOne-Gold, while XP-EndoShaper did not significantly increase root canal volume during preparation.

Poly-(lactic acid) and fibrin bioactive cellularized scaffold for use in bone regenerative medicine: Proof of concept

2021 ◽  
pp. 088391152199640
Author(s):  
Renata Aquino de Carvalho ◽  
Valmir Vieira Rocha Júnior ◽  
Antonio José Felix Carvalho ◽  
Heloisa Sobreiro Selistre de Araújo ◽  
Mônica Rosas Costa Iemma ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Regenerative Medicine ◽  
Platelet Rich Plasma ◽  
Three Dimensional ◽  
Culture Conditions ◽  
Infrapatellar Fat Pad ◽  
Dimensional Structure ◽  
Poly Lactic Acid ◽  
Proof Of Concept ◽  
Critical Bone Defects

Bone regenerative medicine (BRM) aims to overcome the limitations of conventional treatments for critical bone defects by developing therapeutic strategies, based on temporary bioactive substitutes, capable of stimulating, sustaining, and guiding tissue regeneration. The aim of this study was to validate the “proof of concept” of a cellularized bioactive scaffold and establish its potential for use in BRM. For this purpose, three-dimensional scaffolds of poly-(lactic acid) (PLA), produced by the additive manufacturing technique, were incorporated into a human platelet-rich plasma (PRP-h) fibrin matrix containing human infrapatellar fat pad mesenchymal stem cells (hIFPMSC). The scaffolds (PLA/finbrin-bioactive) were kept under ideal culture conditions in a medium free from fetal bovine serum and analyzed at 5 and 10 days by Scanning Electron Microscopy (SEM), Fourrier Transform Infrared (FTIR), Circular Dichroism and fluorescence microscopy. The results demonstrated the feasibility of obtaining a rigid, cytocompatible, and cellularized three-dimensional structure. In addition, PRP platelets and leukocytes were able to provide a bioactive environment capable of maintaining the viability of hIFPMSC into scaffolds. The results validate the concept of a customizable, bioactive, cellularized, and non-immunogenic strategy for application in BRM.

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