scholarly journals Estimation of the interpolation error of a three-step rotation algorithm using recorded images with rotated test pattern as ground truth

2017 ◽  
Vol 3 (2) ◽  
pp. 555-558
Author(s):  
Elisa Dicke ◽  
Andreas Wachter ◽  
Werner Nahm
Keyword(s):  
3D Reconstruction ◽  
Test Pattern ◽  
Surgical Navigation ◽  
Three Dimensional ◽  
Ground Truth ◽  
Interpolation Error ◽  
Navigation Data ◽  
One Step ◽  
Final Adjustment ◽  
Recorded Image

AbstractNowadays, the surgical microscope is the goldstandard for microsurgical procedures. Additional functionalities such as surgical navigation, data injection or imageoverlay are providing additional valuable information to the surgeon. For substituting the conventional optical system by a fully-digital multi-camera setup the three dimensional (3D) reconstruction of the scenery in the field of view is required. However, for in camera-based systems, an exact alignment of the cameras is a challenging task. Therefore, a final adjustment through a digital image rotation becomes necessary. Even though the digital rotation is a commonly used procedure, it leads to unavoidable errors because of the discretized grid of the image. Previous research reported in literature has demonstrated that the method of digitally rotating the images combined with the Fourier interpolation delivers the results of best quality. Nevertheless, the performance evaluation of this algorithm was carried out rotating an image in multiple threestep rotations to a total of 90 or 180 degrees and comparing it to the original image rotated in one step. This is a valid approach because a rotation of 90 or 180 degrees does not produce rotation artifacts. In this research project, we verify the performance of the three-step rotation algorithm using recorded images for which the test pattern was rotated as ground truth. A series of photographs with a rotation angle of 3 to 45 degrees was created. The advantage of this setup is that the result of the digital rotation can be directly compared to the recorded image. In addition, with the knowledge obtained about the interpolation error, we can improve pixel matching in the further triangulation used for 3D reconstruction. By doing so, the estimation of the interpolation error helps to reduce the triangulation error.

scholarly journals UNI-EM: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hidetoshi Urakubo ◽  
Torsten Bullmann ◽  
Yoshiyuki Kubota ◽  
Shigeyuki Oba ◽  
Shin Ishii
Keyword(s):  
Image Segmentation ◽  
3D Reconstruction ◽  
Three Dimensional ◽  
Ground Truth ◽  
Rapid Expansion ◽  
Deep Convolutional Neural Networks ◽  
Electron Microscopic ◽  
Ground Truth Generation ◽  
3D Cnn ◽  
2D And 3D

AbstractRecently, there has been rapid expansion in the field of micro-connectomics, which targets the three-dimensional (3D) reconstruction of neuronal networks from stacks of two-dimensional (2D) electron microscopy (EM) images. The spatial scale of the 3D reconstruction increases rapidly owing to deep convolutional neural networks (CNNs) that enable automated image segmentation. Several research teams have developed their own software pipelines for CNN-based segmentation. However, the complexity of such pipelines makes their use difficult even for computer experts and impossible for non-experts. In this study, we developed a new software program, called UNI-EM, for 2D and 3D CNN-based segmentation. UNI-EM is a software collection for CNN-based EM image segmentation, including ground truth generation, training, inference, postprocessing, proofreading, and visualization. UNI-EM incorporates a set of 2D CNNs, i.e., U-Net, ResNet, HighwayNet, and DenseNet. We further wrapped flood-filling networks (FFNs) as a representative 3D CNN-based neuron segmentation algorithm. The 2D- and 3D-CNNs are known to demonstrate state-of-the-art level segmentation performance. We then provided two example workflows: mitochondria segmentation using a 2D CNN and neuron segmentation using FFNs. By following these example workflows, users can benefit from CNN-based segmentation without possessing knowledge of Python programming or CNN frameworks.

scholarly journals UNI-EM: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images

2019 ◽  
Author(s):  
Hidetoshi Urakubo ◽  
Torsten Bullmann ◽  
Yoshiyuki Kubota ◽  
Shigeyuki Oba ◽  
Shin Ishii
Keyword(s):  
Image Segmentation ◽  
3D Reconstruction ◽  
Three Dimensional ◽  
Ground Truth ◽  
Rapid Expansion ◽  
Electron Microscopic ◽  
Research Teams ◽  
Ground Truth Generation ◽  
Python Programming ◽  
2D And 3D

AbstractRecently, there has been a rapid expansion in the field of micro-connectomics, which targets the three-dimensional (3D) reconstruction of neuronal networks from a stack of two-dimensional (2D) electron microscopic (EM) images. The spatial scale of the 3D reconstruction grows rapidly owing to deep neural networks (DNNs) that enable automated image segmentation. Several research teams have developed their own software pipelines for DNN-based segmentation. However, the complexity of such pipelines makes their use difficult even for computer experts and impossible for non-experts. In this study, we developed a new software program, called UNI-EM, that enables 2D- and 3D-DNN-based segmentation for non-computer experts. UNI-EM is a software collection for DNN-based EM image segmentation, including ground truth generation, training, inference, postprocessing, proofreading, and visualization. UNI-EM comes with a set of 2D DNNs, i.e., U-Net, ResNet, HighwayNet, and DenseNet. We further wrapped flood-filling networks (FFNs) as a representative 3D DNN-based neuron segmentation algorithm. The 2D- and 3D-DNNs are known to show state-of-the-art level segmentation performance. We then provided two-example workflows: mitochondria segmentation using a 2D DNN as well as neuron segmentation using FFNs. Following these example workflows, users can benefit from DNN-based segmentation without any knowledge of Python programming or DNN frameworks.

scholarly journals Three-Dimensional Reconstruction of Light Field Based on Phase Similarity

Sensors ◽  
2021 ◽  
Vol 21 (22) ◽  
pp. 7734
Author(s):  
Wei Feng ◽  
Junhui Gao ◽  
Tong Qu ◽  
Shiqi Zhou ◽  
Daxing Zhao
Keyword(s):  
3D Reconstruction ◽  
Light Field ◽  
Three Dimensional ◽  
Ground Truth ◽  
Depth Estimation ◽  
Estimation Algorithm ◽  
Morphological Processing ◽  
Disparity Estimation ◽  
Reconstruction Method ◽  
Disparity Map

Light field imaging plays an increasingly important role in the field of three-dimensional (3D) reconstruction because of its ability to quickly obtain four-dimensional information (angle and space) of the scene. In this paper, a 3D reconstruction method of light field based on phase similarity is proposed to increase the accuracy of depth estimation and the scope of applicability of epipolar plane image (EPI). The calibration method of the light field camera was used to obtain the relationship between disparity and depth, and the projector calibration was removed to make the experimental procedure more flexible. Then, the disparity estimation algorithm based on phase similarity was designed to effectively improve the reliability and accuracy of disparity calculation, in which the phase information was used instead of the structure tensor, and the morphological processing method was used to denoise and optimize the disparity map. Finally, 3D reconstruction of the light field was realized by combining disparity information with the calibrated relationship. The experimental results showed that the reconstruction standard deviation of the two objects was 0.3179 mm and 0.3865 mm compared with the ground truth of the measured objects, respectively. Compared with the traditional EPI method, our method can not only make EPI perform well in a single scene or blurred texture situations but also maintain good reconstruction accuracy.

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.

Controllable Electrochemical Synthesis of Ag Hierarchical Micro/Nanostructures with High SERS-Activity

NANO ◽  
2020 ◽  
Vol 15 (04) ◽  
pp. 2050043
Author(s):  
Huayu Zhou ◽  
Jingjing Wang ◽  
Qiong Yang ◽  
Menglei Chen ◽  
Changsheng Song ◽  
...  
Keyword(s):  
Indium Tin Oxide ◽  
Current System ◽  
Three Dimensional ◽  
Constant Current ◽  
Localized Surface Plasmon ◽  
Excitation Wavelength ◽  
Raman Signal ◽  
Mixed Solution ◽  
Raman Enhancement ◽  
One Step

We report a one-step electrochemical deposition technique to prepare three-dimensional (3D) Ag hierarchical micro/nanostructured film consisting of well-crystallized Ag nanosheets grown on an indium tin oxide (ITO) conductive substrate. The Ag hierarchical micro/nanostructures were fabricated in the mixed solution of AgNO3 and sodium citrate in a constant current system at room temperature. Through reduction of Ag[Formula: see text] electrodeposited on the surface of ITO substrate, nanoparticles were grown to form nanosheets which further combined into 3D sphere-like microstructures. The 3D Ag micro/nanostructures have many sharp edges and nanoscale gaps which can give rise to good Raman-enhanced effect. Due to localized surface plasmon resonance (LSPR) effects, these special Ag micro/nanostructures exhibited good Raman-enhanced performance. Using Rhodamine 6G (R6G) molecules as probe molecule, we studied the influence of excitation wavelength on Raman enhancement. The results showed that the 532[Formula: see text]nm excitation wavelength is the best to obtain the strongest Raman signal and to reduce the influence of other impurity peaks. Using the as-synthesized Ag hierarchical micro/nanostructures, we can detect the 10[Formula: see text][Formula: see text]mol/L R6G aqueous solution, exhibiting great Raman-enhanced effect.

scholarly journals A Review on Additive Manufacturing Possibilities for Electrical Machines

Energies ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 1940
Author(s):  
Muhammad Usman Naseer ◽  
Ants Kallaste ◽  
Bilal Asad ◽  
Toomas Vaimann ◽  
Anton Rassõlkin
Keyword(s):  
Additive Manufacturing ◽  
Large Scale ◽  
Three Dimensional ◽  
Electrical Machines ◽  
Electromagnetic Properties ◽  
Scale Production ◽  
Performance Parameters ◽  
Large Scale Production ◽  
One Step ◽  
Manufacturing Techniques

This paper presents current research trends and prospects of utilizing additive manufacturing (AM) techniques to manufacture electrical machines. Modern-day machine applications require extraordinary performance parameters such as high power-density, integrated functionalities, improved thermal, mechanical & electromagnetic properties. AM offers a higher degree of design flexibility to achieve these performance parameters, which is impossible to realize through conventional manufacturing techniques. AM has a lot to offer in every aspect of machine fabrication, such that from size/weight reduction to the realization of complex geometric designs. However, some practical limitations of existing AM techniques restrict their utilization in large scale production industry. The introduction of three-dimensional asymmetry in machine design is an aspect that can be exploited most with the prevalent level of research in AM. In order to take one step further towards the enablement of large-scale production of AM-built electrical machines, this paper also discusses some machine types which can best utilize existing developments in the field of AM.

scholarly journals Is Dialdehyde Chitosan a Good Substance to Modify Physicochemical Properties of Biopolymeric Materials?

2021 ◽  
Vol 22 (7) ◽  
pp. 3391
Author(s):  
Sylwia Grabska-Zielińska ◽  
Alina Sionkowska ◽  
Ewa Olewnik-Kruszkowska ◽  
Katarzyna Reczyńska ◽  
Elżbieta Pamuła
Keyword(s):  
Mechanical Properties ◽  
Tissue Engineering ◽  
Physicochemical Properties ◽  
Silk Fibroin ◽  
Three Dimensional ◽  
Microscopy Imaging ◽  
Maximum Deformation ◽  
One Step ◽  
Chitosan Blends ◽  
Fourier Transfer Infrared Spectroscopy

The aim of this work was to compare physicochemical properties of three dimensional scaffolds based on silk fibroin, collagen and chitosan blends, cross-linked with dialdehyde starch (DAS) and dialdehyde chitosan (DAC). DAS was commercially available, while DAC was obtained by one-step synthesis. Structure and physicochemical properties of the materials were characterized using Fourier transfer infrared spectroscopy with attenuated total reflectance device (FTIR-ATR), swelling behavior and water content measurements, porosity and density observations, scanning electron microscopy imaging (SEM), mechanical properties evaluation and thermogravimetric analysis. Metabolic activity with AlamarBlue assay and live/dead fluorescence staining were performed to evaluate the cytocompatibility of the obtained materials with MG-63 osteoblast-like cells. The results showed that the properties of the scaffolds based on silk fibroin, collagen and chitosan can be modified by chemical cross-linking with DAS and DAC. It was found that DAS and DAC have different influence on the properties of biopolymeric scaffolds. Materials cross-linked with DAS were characterized by higher swelling ability (~4000% for DAS cross-linked materials; ~2500% for DAC cross-linked materials), they had lower density (Coll/CTS/30SF scaffold cross-linked with DAS: 21.8 ± 2.4 g/cm3; cross-linked with DAC: 14.6 ± 0.7 g/cm3) and lower mechanical properties (maximum deformation for DAC cross-linked scaffolds was about 69%; for DAS cross-linked scaffolds it was in the range of 12.67 ± 1.51% and 19.83 ± 1.30%) in comparison to materials cross-linked with DAC. Additionally, scaffolds cross-linked with DAS exhibited higher biocompatibility than those cross-linked with DAC. However, the obtained results showed that both types of scaffolds can provide the support required in regenerative medicine and tissue engineering. The scaffolds presented in the present work can be potentially used in bone tissue engineering to facilitate healing of small bone defects.

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.

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