PerfectTailor: Scale-Preserving 2D Pattern Adjustment Driven by 3D Garment Editing.

We address the problem of modifying a given well-designed 2D sewing pattern to accommodate garment edits in the 3D space. Existing methods usually adjust the sewing pattern by applying uniform flattening to the 3D garment. The problems are twofold: first, it ignores local scaling of the 2D sewing pattern such as shrinking ribs of cuffs; second, it does not respect the implicit design rules and conventions of the industry, such as the use of straight edges for simplicity and precision in sewing. To address those problems, we present a pattern adjustment method that considers the non-uniform local scaling of the 2D sewing pattern by utilizing the intrinsic scale matrix. In addition, we preserve the original boundary shape by an as-original-as-possible geometric constraint when desirable. We build a prototype with a set of commonly used alteration operations and showcase the capability of our method via a number of alteration examples throughout the paper.

Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows.

BACKGROUND: Many open-source workflow systems have made bioinformatics data analysis procedures portable. Sharing these workflows provides researchers easy access to high-quality analysis methods without the requirement of computational expertise. However, published workflows are not always guaranteed to be reliably reusable. Therefore, a system is needed to lower the cost of sharing workflows in a reusable form. RESULTS: We introduce Yevis, a system to build a workflow registry that automatically validates and tests workflows to be published. The validation and test are based on the requirements we defined for a workflow being reusable with confidence. Yevis runs on GitHub and Zenodo and allows workflow hosting without the need of dedicated computing resources. A Yevis registry accepts workflow registration via a GitHub pull request, followed by an automatic validation and test process for the submitted workflow. As a proof of concept, we built a registry using Yevis to host workflows from a community to demonstrate how a workflow can be shared while fulfilling the defined requirements. CONCLUSIONS: Yevis helps in the building of a workflow registry to share reusable workflows without requiring extensive human resources. By following Yevis's workflow-sharing procedure, one can operate a registry while satisfying the reusable workflow criteria. This system is particularly useful to individuals or communities that want to share workflows but lacks the specific technical expertise to build and maintain a workflow registry from scratch.

A workflow reproducibility scale for automatic validation of biological interpretation results.

BACKGROUND: Reproducibility of data analysis workflow is a key issue in the field of bioinformatics. Recent computing technologies, such as virtualization, have made it possible to reproduce workflow execution with ease. However, the reproducibility of results is not well discussed; that is, there is no standard way to verify whether the biological interpretation of reproduced results is the same. Therefore, it still remains a challenge to automatically evaluate the reproducibility of results. RESULTS: We propose a new metric, a reproducibility scale of workflow execution results, to evaluate the reproducibility of results. This metric is based on the idea of evaluating the reproducibility of results using biological feature values (e.g., number of reads, mapping rate, and variant frequency) representing their biological interpretation. We also implemented a prototype system that automatically evaluates the reproducibility of results using the proposed metric. To demonstrate our approach, we conducted an experiment using workflows used by researchers in real research projects and the use cases that are frequently encountered in the field of bioinformatics. CONCLUSIONS: Our approach enables automatic evaluation of the reproducibility of results using a fine-grained scale. By introducing our approach, it is possible to evolve from a binary view of whether the results are superficially identical or not to a more graduated view. We believe that our approach will contribute to more informed discussion on reproducibility in bioinformatics.

Threshold field painting saves the time for segmentation of minute arteries.

PURPOSE: It is often time-consuming to segment fine structures, such as the cerebral arteries from magnetic resonance imaging (MRI). Moreover, extracting anatomically abnormal structures is generally difficult. The segmentation workflow called threshold field painting was tested for its feasibility in morbid minute artery segmentation with special emphasis on time efficiency. METHODS: Seven patients with meningioma with ten-sided feeding arteries (n = 10) originating from middle meningeal arteries (MMA) were investigated by three experts of the conventional method for segmentation. The MRI time-of-flight sequence was utilized for the segmentation of each procedure. The tasks were accomplished using both the conventional method and the proposed method in random order. The task completion time and usability score were analyzed using the Wilcoxon signed-rank test. RESULTS: Except for one examinee (P = 0.06), the completion time significantly decreased (both P < 0.01) with the use of the proposed method. The average task completion time among the three examinees for the conventional method was 2.8 times longer than that for the proposed method. The usability score was generally in favor of the proposed method. CONCLUSION: The normally nonexistent minute arteries, such as the MMA feeders, were deemed more efficiently segmented with the proposed method than with the conventional method. While automatic segmentation might be the ultimate solution, our semiautomatic method incorporating expert knowledge is expected to work as the practical solution.

Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics.

The increased demand for efficient computation in data analysis encourages researchers in biomedical science to use workflow systems. Workflow systems, or so-called workflow languages, are used for the description and execution of a set of data analysis steps. Workflow systems increase the productivity of researchers, specifically in fields that use high-throughput DNA sequencing applications, where scalable computation is required. As systems have improved the portability of data analysis workflows, research communities are able to share workflows to reduce the cost of building ordinary analysis procedures. However, having multiple workflow systems in a research field has resulted in the distribution of efforts across different workflow system communities. As each workflow system has its unique characteristics, it is not feasible to learn every single system in order to use publicly shared workflows. Thus, we developed Sapporo, an application to provide a unified layer of workflow execution upon the differences of various workflow systems. Sapporo has two components: an application programming interface (API) that receives the request of a workflow run and a browser-based client for the API. The API follows the Workflow Execution Service API standard proposed by the Global Alliance for Genomics and Health. The current implementation supports the execution of workflows in four languages: Common Workflow Language, Workflow Description Language, Snakemake, and Nextflow. With its extensible and scalable design, Sapporo can support the research community in utilizing valuable resources for data analysis.

Global Beautification of 2D and 3D Layouts With Interactive Ambiguity Resolution.

Specifying precise relationships among graphic elements is often a time-consuming process with traditional alignment tools. Automatic beautification of roughly designed layouts can provide a more efficient solution but often lead to undesired results due to ambiguity problems. To facilitate ambiguity resolution in layout beautification, we present a novel user interface for visualizing and editing inferred relationships through an automatic global layout beautification process. First, our interface provides a preview of the beautified layout with inferred constraints without directly modifying an input layout. In this way, the user can easily keep refining beautification results by interactively repositioning and/or resizing elements in the input layout. Second, we present a gestural interface for editing automatically inferred constraints by directly interacting with the visualized constraints via simple gestures. Our technique is applicable to both 2D and 3D global layout beautification, supported by efficient system implementation that provides instant user feedback. Our user study validates that our tool is capable of creating, editing, and refining layouts of graphic elements, and is significantly faster than the standard snap-dragging or command-based alignment tools for both 2D and 3D layout tasks.

Simulating Liquids on Dynamically Warping Grids.

We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.

RoboJockey: Designing an Entertainment Experience with Robots.

The RoboJockey entertainment system consists of a multitouch tabletop interface for multiuser collaboration. RoboJockey enables a user to choreograph a mobile robot or a humanoid robot by using a simple visual language. With RoboJockey, a user can coordinate the mobile robot's actions with a combination of back, forward, and rotating movements and coordinate the humanoid robot's actions with a combination of arm and leg movements. Every action is automatically performed to background music. RoboJockey was demonstrated to the public during two pilot studies, and the authors observed users' behavior. Here, they report the results of their observations and discuss the RoboJockey entertainment experience.

A Sketching Interface for Sitting Pose Design in the Virtual Environment.

Character pose design is one of the most fundamental processes in computer graphics authoring. Although there are many research efforts in this field, most existing design tools consider only character body structure, rather than its interaction with the environment. This paper presents an intuitive sketching interface that allows the user to interactively place a 3D human character in a sitting position on a chair. Within our framework, the user sketches the target pose as a 2D stick figure and attaches the selected joints to the environment (e.g., the feet on the ground) with a pin tool. As reconstructing the 3D pose from a 2D stick figure is an ill-posed problem due to many possible solutions, the key idea in our paper is to reduce solution space by considering the interaction between the character and environment and adding physics constraints, such as balance and collision. Further, we formulated this reconstruction into a nonlinear optimization problem and solved it via the genetic algorithm (GA) and the quasi-Newton solver. With the GPU implementation, our system is able to generate the physically correct and visually pleasing pose at an interactive speed. The promising experimental results and user study demonstrates the efficacy of our method.

A kinematic approach for efficient and robust simulation of the cardiac beating motion.

Computer simulation techniques for cardiac beating motions potentially have many applications and a broad audience. However, most existing methods require enormous computational costs and often show unstable behavior for extreme parameter sets, which interrupts smooth simulation study and make it difficult to apply them to interactive applications. To address this issue, we present an efficient and robust framework for simulating the cardiac beating motion. The global cardiac motion is generated by the accumulation of local myocardial fiber contractions. We compute such local-to-global deformations using a kinematic approach; we divide a heart mesh model into overlapping local regions, contract them independently according to fiber orientation, and compute a global shape that satisfies contracted shapes of all local regions as much as possible. A comparison between our method and a physics-based method showed that our method can generate motion very close to that of a physics-based simulation. Our kinematic method has high controllability; the simulated ventricle-wall-contraction speed can be easily adjusted to that of a real heart by controlling local contraction timing. We demonstrate that our method achieves a highly realistic beating motion of a whole heart in real time on a consumer-level computer. Our method provides an important step to bridge a gap between cardiac simulations and interactive applications.

Holly: a drawing editor for designing stencils.

Designing a stencil is difficult because of the requirement that all positive regions are connected. In this proposed method for generating expressive stencils, you simply use standard drawing operations, and the system automatically generates the appropriate stencil satisfying that constraint. You obtain the physical stencil by sending the result to a cutting plotter. Finally, you use the stencil to decorate the target object (for example, fabric or a postcard). In a workshop for novices, even children could design their own stencils using this system. The Web extra is a video shows how the Holly system lets users easily design valid stencils from scratch.

A procedural method for modeling the purkinje fibers of the heart.

The Purkinje fibers are located in the ventricular walls of the heart, just beneath the endocardium and conduct excitation from the right and left bundle branches to the ventricular myocardium. Recently, anatomists succeeded in photographing the Purkinje fibers of a sheep, which clearly showed the mesh structure of the Purkinje fibers. In this study, we present a technique for modeling the mesh structure of Purkinje fibers semiautomatically using an extended L-system. The L-system is a formal grammar that defines the growth of a fractal structure by generating rules (or rewriting rules) and an initial structure. It was originally formulated to describe the growth of plant cells, and has subsequently been applied for various purposes in computer graphics such as modeling plants, buildings, streets, and ornaments. For our purpose, we extended the growth process of the L-system as follows: 1) each growing branch keeps away from existing branches as much as possible to create a uniform distribution, and 2) when branches collide, we connect the colliding branches to construct a closed mesh structure. We designed a generating rule based on observations of the photograph of Purkinje fibers and manually specified three terminal positions on a three-dimensional (3D) heart model: those of the right bundle branch, the anterior fascicle, and the left posterior fascicle of the left branch. Then, we grew fibers starting from each of the three positions based on the specified generating rule. We achieved to generate 3D models of Purkinje fibers of which physical appearances closely resembled the real photograph. The generation takes a few seconds. Variations of the Purkinje fibers could be constructed easily by modifying the generating rules and parameters.

A sketch-based interface for modeling myocardial fiber orientation that considers the layered structure of the ventricles.

We propose a sketch-based interface for modeling the myocardial fiber orientation required in the electrophysiological simulation of the heart, especially the ventricles. The user can create a volumetric vector field that represents the myocardial fiber orientation in two steps. First, a depth field over the three-dimensional (3D) ventricular model is defined to create layers of myocardium. The user can then peel these layers and draw strokes on them to specify the myocardial fiber orientation in each layer. We represent the 3D ventricular model as a tetrahedral mesh and perform Laplacian smoothing over the mesh vertices to interpolate the vector field defined by the user-drawn strokes. Our method also allows the user to perform deformations on volumetric models of myocardial fiber orientation, which is very important for studying heart disease associated with morphological abnormalities. We created several examples of myocardial fiber orientation and applied them to a simplified simulator to demonstrate the effectiveness of our method.