Synthetic 3D Pap smear nucleus generation

Gómez Aguilar, S. (2010). Synthetic 3D Pap smear nucleus generation. http://hdl.handle.net/10251/10215.Archivo delegad

3D Object Reconstruction from Imperfect Depth Data Using Extended YOLOv3 Network

State-of-the-art intelligent versatile applications provoke the usage of full 3D, depth-based streams, especially in the scenarios of intelligent remote control and communications, where virtual and augmented reality will soon become outdated and are forecasted to be replaced by point cloud streams providing explorable 3D environments of communication and industrial data. One of the most novel approaches employed in modern object reconstruction methods is to use a priori knowledge of the objects that are being reconstructed. Our approach is different as we strive to reconstruct a 3D object within much more difficult scenarios of limited data availability. Data stream is often limited by insufficient depth camera coverage and, as a result, the objects are occluded and data is lost. Our proposed hybrid artificial neural network modifications have improved the reconstruction results by 8.53 which allows us for much more precise filling of occluded object sides and reduction of noise during the process. Furthermore, the addition of object segmentation masks and the individual object instance classification is a leap forward towards a general-purpose scene reconstruction as opposed to a single object reconstruction task due to the ability to mask out overlapping object instances and using only masked object area in the reconstruction process

Phase Field Model for Three-Dimensional Dendritic Growth with Fluid Flow

We study the effect of fluid flow on three-dimensional (3D) dendrite growth using a phase-field model on an adaptive finite element grid. In order to simulate 3D fluid flow, we use an averaging method for the flow problem coupled to the phase-field method and the Semi-Implicit Approximated Projection Method (SIAPM). We describe a parallel implementation for the algorithm, using Charm++ FEM framework, and demonstrate its efficiency. We introduce an improved method for extracting dendrite tip position and tip radius, facilitating accurate comparison to theory. We benchmark our results for two-dimensional (2D) dendrite growth with solvability theory and previous results, finding them to be in good agreement. The physics of dendritic growth with fluid flow in three dimensions is very different from that in two dimensions, and we discuss the origin of this behavior

EPiK-a Workflow for Electron Tomography in Kepler.

Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility