- Browse by Subject
Browsing by Subject "Three-dimensional imaging"
Now showing 1 - 10 of 16
Results Per Page
Sort Options
Item A 2D PLUS DEPTH VIDEO CAMERA PROTOTYPE USING DEPTH FROM DEFOCUS IMAGING AND A SINGLE MICROFLUIDIC LENS(2011-08) Li, Weixu; Christopher, Lauren; Rizkalla, Maher E.; Salama, PaulA new method for capturing 3D video from a single imager and lens is introduced in this research. The benefit of this method is that it does not have the calibration and alignment issues associated with binocular 3D video cameras, and allows for a less expensive overall system. The digital imaging technique Depth from Defocus (DfD) has been successfully used in still camera imaging to develop a depth map associated with the image. However, DfD has not been applied in real-time video so far since the focus mechanisms are too slow to produce real-time results. This new research result shows that a Microfluidic lens is capable of the required focal length changes at 2x video frame rate, due to the electrostatic control of the focus. During the processing, two focus settings per output frame are captured using this lens combined with a broadcast video camera prototype. We show that the DfD technique using Bayesian Markov Random Field optimization can produce a valid depth map.Item 3D Assessment of Nasopharyngeal and Craniofacial Phenotypes in Ts65Dn Down Syndrome Mice Treated with a Dyrk1a Inhibitor(2014-04-11) Starbuck, John M.; Harrington, Emily; Kula, Katherine S.; Ghoneima, Ahmed A.; Roper, Randall J.Background: Down syndrome (DS) originates from having three copies of chromosome 21 (i.e. Trisomy 21). DS is associated with many detrimental phenotypes including intellectual disabilities, heart defects, abnormal craniofacial development, and obstructive sleep apnea, which develops from restricted nasopharyngeal airways and an underdeveloped mandible. Ts65Dn mice are trisomic for about half of the orthologs on human chromosome 21 and display many phenotypes associated with DS including craniofacial abnormalities. Dyrk1a is found in three copies in Ts65Dn mice and individuals with DS, and thought to be a root cause of the craniofacial phenotypes. Epigallocatechin 3-gallate (EGCG) is a green tea polyphenol and inhibitor of Dyrk1a activity. Purpose: We hypothesize that decreased Dyrk1a activity in Ts65Dn mice will ameliorate craniofacial dysmorphology. Methods: To test our hypothesis we compared Ts65Dn mice with two or three copies of Dyrk1a and compared Ts65Dn mice with and without prenatal EGCG treatment. EGCG treated mothers were fed 200mg/kg EGCG on gestational day 7. Six week old mice were sacrificed and their heads imaged using micro-computed tomography (μCT). From μCT images, we measured nasopharyngeal airway volume and anatomical landmarks (n = 54) from the facial skeleton, cranial vault, cranial base, and mandible. Mean nasopharyngeal airway volumes were graphically compared, and a landmark-based multivariate geometric morphometric approach known as Euclidean Distance Matrix Analysis (EDMA) was carried out to assess local differences in craniofacial morphology between trisomic mouse samples. Results: Our preliminary results indicate that EGCG treatment and reduced Dyrk1a copy number increases mean nasopharyngeal airway volume in Ts65Dn mice. Craniofacial morphometric differences were found among all samples. EGCG treatment increased portions of the mandible and decreased portions of the cranial vault and cranial base. Conclusion: Preliminary analyses suggest that both EGCG treatment and reduced Dyrk1a copy number affect craniofacial morphology.Item 3D ENDOSCOPY VIDEO GENERATED USING DEPTH INFERENCE: CONVERTING 2D TO 3D(2013-08-20) Rao, Swetcha; Christopher, Lauren; Rizkalla, Maher E.; Salama, Paul; King, BrianA novel algorithm was developed to convert raw 2-dimensional endoscope videos into 3-dimensional view. Minimally invasive surgeries aided with 3D view of the invivo site have shown to reduce errors and improve training time compared to those with 2D view. The novelty of this algorithm is that two cues in the images have been used to develop the 3D. Illumination is the rst cue used to nd the darkest regions in the endoscopy images in order to locate the vanishing point(s). The second cue is the presence of ridge-like structures in the in-vivo images of the endoscopy image sequence. Edge detection is used to map these ridge-like structures into concentric ellipses with their common center at the darkest spot. Then, these two observations are used to infer the depth of the endoscopy videos; which then serves to convert them from 2D to 3D. The processing time is between 21 seconds to 20 minutes for each frame, on a 2.27GHz CPU. The time depends on the number of edge pixels present in the edge-detection image. The accuracy of ellipse detection was measured to be 98.98% to 99.99%. The algorithm was tested on 3 truth images with known ellipse parameters and also on real bronchoscopy image sequences from two surgical procedures. Out of 1020 frames tested in total, 688 frames had single vanishing point while 332 frames had two vanishing points. Our algorithm detected the single vanishing point in 653 of the 688 frames and two vanishing points in 322 of the 332 frames.Item 3D Image Segmentation Implementation on FPGA Using EM/MPM Algorithm(2010-12) Sun, Yan; Christopher, Lauren; Rizkalla, Maher E.; Salama, PaulIn this thesis, 3D image segmentation is targeted to a Xilinx Field Programmable Gate Array (FPGA), and verified with extensive simulation. Segmentation is performed using the Expectation-Maximization with Maximization of the Posterior Marginals (EM/MPM) Bayesian algorithm. This algorithm segments the 3D image using neighboring pixels based on a Markov Random Field (MRF) model. This iterative algorithm is designed, synthesized and simulated for the Xilinx FPGA, and greater than 100 times speed improvement over standard desktop computer hardware is achieved. Three new techniques were the key to achieving this speed: Pipelined computational cores, sixteen parallel data paths and a novel memory interface for maximizing the external memory bandwidth. Seven MPM segmentation iterations are matched to the external memory bandwidth required of a single source file read, and a single segmented file write, plus a small amount of latency.Item 3D Scanning for Small Budgets: How Local Libraries and Museums Will Play a Role in Creating a 3D Digital Library(2015-12-15) Johnson, Jennifer; Schaumberg, JDIndiana University–Purdue University Indianapolis (IUPUI) University Library has been digitizing and providing access to community and cultural heritage collections since 2006. Varying formats include: audio, video, photographs, slides, negatives, and text (bound, loose). The library provides access to these collections using CONTENTdm. As 3D technologies become increasingly popular in libraries and museums, IUPUI University Library is exploring the workflows and processes as they relate to 3D artifacts. The library is collaborating with Online Resources Inc., a company that specializes in 3D technology to digitize artifacts from the Benjamin Harrison Presidential Site. Online Resources has seen the high prices and complexity of systems hinder entrance into 3D data collection. They have made great strides in cost reduction for small budgets, and clarifying the best scanning system for the job. This presentation will demonstrate Creaform’s Go!Scan 3D while discussing collection digitization for small museums. Presenters will share insight on: key terms and features, how to filter to the correct 3D scanner, and how to reduce the cost of 3D scanning. This session will include discussion of how this technology may be implemented at the local level.Item Active geometric model : multi-compartment model-based segmentation & registration(2014-08-26) Mukherjee, Prateep; Tsechpenakis, Gavriil; Raje, Rajeev; Tuceryan, MihranWe present a novel, variational and statistical approach for model-based segmentation. Our model generalizes the Chan-Vese model, proposed for concurrent segmentation of multiple objects embedded in the same image domain. We also propose a novel shape descriptor, namely the Multi-Compartment Distance Functions or mcdf. Our proposed framework for segmentation is two-fold: first, several training samples distributed across various classes are registered onto a common frame of reference; then, we use a variational method similar to Active Shape Models (or ASMs) to generate an average shape model and hence use the latter to partition new images. The key advantages of such a framework is: (i) landmark-free automated shape training; (ii) strict shape constrained model to fit test data. Our model can naturally deal with shapes of arbitrary dimension and topology(closed/open curves). We term our model Active Geometric Model, since it focuses on segmentation of geometric shapes. We demonstrate the power of the proposed framework in two important medical applications: one for morphology estimation of 3D Motor Neuron compartments, another for thickness estimation of Henle's Fiber Layer in the retina. We also compare the qualitative and quantitative performance of our method with that of several other state-of-the-art segmentation methods.Item Exploring 3D Scanning for the Creation of Digital Cultural Heritage Collections(2015-10-26) Schaumberg, JD; Proctor, Anna; Johnson, JenniferIUPUI University Library has been digitizing and providing access to community and cultural heritage collections since 2006. Varying formats include: audio, video, photographs, slides, negatives, and text (bound, loose). The library provides access to these collections using CONTENTdm. As 3D technologies become increasingly popular in libraries and museums, IUPUI University Library is exploring the workflows and processes as they relate to 3D artifacts. The library is collaborating with Online Resources Inc., a company that specializes in 3D technology to explore new ways to deliver content to a digital audience.Item Inclusion of 3D Artifacts into a Digital Library: Exploring Technologies and Best Practice Techniques(2016-11-08) Johnson, Jennifer; Proctor, AnnaAdvances in 3D technologies are providing libraries and museums the opportunity to capture 3D artifacts in digital formats. The Center for Digital Scholarship at IUPUI University Library is implementing workflows and determining best practices to incorporate 3D images into an already established digital library of community and cultural heritage collections.Item Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline(Elsevier, 2021) Ferkowicz, Michael J.; Winfree, Seth; Sabo, Angela R.; Kamocka, Malgorzata M.; Khochare, Suraj; Barwinska, Daria; Eadon, Michael T.; Cheng, Ying-Hua; Phillips, Carrie L.; Sutton, Timothy A.; Kelly, Katherine J.; Dagher, Pierre C.; El-Achkar, Tarek M.; Dunn, Kenneth W.; Kidney Precision Medicine Project; Anatomy, Cell Biology and Physiology, School of MedicineThe advent of personalized medicine has driven the development of novel approaches for obtaining detailed cellular and molecular information from clinical tissue samples. Tissue cytometry is a promising new technique that can be used to enumerate and characterize each cell in a tissue and, unlike flow cytometry and other single-cell techniques, does so in the context of the intact tissue, preserving spatial information that is frequently crucial to understanding a cell's physiology, function, and behavior. However, the wide-scale adoption of tissue cytometry as a research tool has been limited by the fact that published examples utilize specialized techniques that are beyond the capabilities of most laboratories. Here we describe a complete and accessible pipeline, including methods of sample preparation, microscopy, image analysis, and data analysis for large-scale three-dimensional tissue cytometry of human kidney tissues. In this workflow, multiphoton microscopy of unlabeled tissue is first conducted to collect autofluorescence and second-harmonic images. The tissue is then labeled with eight fluorescent probes, and imaged using spectral confocal microscopy. The raw 16-channel images are spectrally deconvolved into 8-channel images, and analyzed using the Volumetric Tissue Exploration and Analysis (VTEA) software developed by our group. We applied this workflow to analyze millimeter-scale tissue samples obtained from human nephrectomies and from renal biopsies from individuals diagnosed with diabetic nephropathy, generating a quantitative census of tens of thousands of cells in each. Such analyses can provide useful insights that can be linked to the biology or pathology of kidney disease. The approach utilizes common laboratory techniques, is compatible with most commercially-available confocal microscope systems and all image and data analysis is conducted using the VTEA image analysis software, which is available as a plug-in for ImageJ.Item Mathematical analysis of the lithium ion transport in lithium ion batteries using three dimensional reconstructed electrodes(2012-05) Lim, Cheol Woong; Zhu, Likun; Xie, Jian; Kim, Youngsik; Anwar, SohelComputational analysis of lithium ion batteries has been improved since Newman and et al. suggested the porous electrode theory. It assumed the electrode as a simple structure of homogeneous spherical particles. Bruggeman relationship which characterizes porous material by a simple equation was adopted in the homogeneous electrode model instead of the electrode morphology. To improve the prediction of a cell performance, the numerical analysis requires the realistic microstructure of the cell. Based on the experimentally determined microstructure of the positive and negative electrodes of a lithium ion battery (LIB) using x-ray micro/nano-CT technology, three dimensional (3D) simulations have been presented in this research. Tortuosity of the microstructures has been calculated by a linear diffusion equation to characterize the 3D morphology. The obtained tortuosity and porosity results pointed out that the Bruggeman relationship is not sufficiently estimate the tortuosity by the porosity of electrodes. We studied the diffusion-induced stress numerically based on realistic morphology of reconstructed particles during the lithium ion intercalation process. Diffusion-induced stresses were simulated at different C rates under galvonostatic conditions and compared with spherical particles. The simulation results showed that the intercalation stresses of particles depend on their geometric characteristics. The highest von Mises stress and tresca stress in a real particle are several times higher than the stresses in a spherical particle with the same volume. With the reconstructed positive electrode structure, local effects in the LIB cathode electrode during galvanostatic discharge process have been studied. The simulation results reported that large current density usually occurs at the joints between cathode active material particles and in the small channels in electrolyte, which will generate high electric joule power. By using the 3D real image of a LIB cathode electrode, numerical simulation results revealed that the spatial distribution of variable fields such as concentration, voltage, reaction rate, overpotential, and etc. in the cathode electrode are complicated and non-uniform, especially at high discharge rates.