Kitware News

First Hackfest Upgrades Girder

In August, Kitware held the first Girder hackfest to enhance the open-source, web-based platform for data management. Over 20 participants attended the all-day hackfest, during which they made a variety of improvements to Girder.

For starters, participants continued to work on a major overhaul of the front-end build infrastructure. Sébastien Barré led this effort, which transitioned the build system for the Girder web client to use Webpack. Webpack allows Girder to ship modular front-end libraries that different applications can easily reuse. Participants also continued to work on a plug-in for a robust Digital Imaging and Communications in Medicine (DICOM) viewer, which integrates directly with the Girder web client.

In addition to their work on existing efforts, participants added several new features to Girder. A new external application template provides a starting point for building custom front-end applications that Girder backs. Another new feature offers administrators the ability to look up files that a specific assetstore manages. The participants also created a modularized Ansible role to easily deploy Girder; a centralized mechanism to manage URL routes in a Girder installation; and a plug-in, slicer_cli, to integrate Girder and Girder Worker with Slicer Execution Model.

In other developments, participants improved data schema validation capabilities on the Girder backend via JavaScript Object Notation (JSON) Schema. They also enhanced the Midas 3 to Girder migration script, and they migrated testing data for the Insight Segmentation and Registration Toolkit (ITK) from https://midas3.kitware.com to https://data.kitware.com.

To try out the upgrades made during the hackfest, please download the latest version of Girder at https://github.com/girder/girder.

Kitware Celebrates Decade in Carrboro

Ten years ago, Stephen Aylward and Julien Jomier opened the first Carrboro, North Carolina, office location for Kitware. Currently, Kitware employs over 30 team members in Carrboro. To accommodate growth, Kitware recently renovated a 10,000 square-foot office space. The space houses an open floor plan with large windows, which overlook the picnic tables and greenery that surround the historic Carr Mill Mall. The renovated space neighbors a yoga studio in downtown Carrboro, where team members can take free classes on Fridays.

The office is also within walking distance of the University of North Carolina at Chapel Hill (UNC), where Aylward and Jomier held positions as faculty members in the department of radiology. While at UNC, they worked closely with Kitware CEO Will Schroeder and with Kitware Vice President and Chief Technical Officer Bill Hoffman on the original development of the Insight Segmentation and Registration Toolkit (ITK). The impact of Kitware and its open-source efforts (such as ITK, CMake, and the Visualization toolkit) in medical image analysis and scientific computing motivated Aylward and Jomier to leave their academic positions and form the Carrboro office. Today, the office continues to have strong ties with its academic roots and with the high-quality students and faculty at UNC.

The employees that Kitware has hired in Carrboro have greatly contributed to the success of the office. The first two employees to join Aylward and Jomier have become leaders at the company: Brad Davis, assistant director of business development, and Patrick Reynolds, technical leader in scientific computing. In 2010, the team hired Deb Howell as an office manager, who has helped to shepherd the distinguished culture at Kitware. The office has also enticed some talent from the company headquarters in New York. Andinet Enquobahrie, assistant director of medical computing, made the move down south in 2009, and Ken Martin, chairman and chief financial officer, moved to Carrboro in 2015.

Since March 2013, the Carrboro office has increased its number of team members by almost 50 percent. This growth has helped it once again secure a place on the list of software developers in the “Triangle Business Journal.” While the office expands, it remains focused on what makes Kitware great: outstanding research and development, combined with amazing software mojo. Jean-Christophe Fillion-Robin and the entire National Alliance for Medical Image Computing (NA-MIC) team, for example, have completely redesigned and reinvigorated 3D Slicer; Matthew McCormick has coordinated, facilitated, and ensured the integrity of ITK; and Zach Mullen has guided the development and adoption of Girder. Thus, although the office once primarily focused on medical computing, it has broadened its expertise to include analytics, scientific visualization, and software processes. The office now serves a range of customers from government agencies such as the National Institutes of Health and the Department of Energy to Fortune 500 companies such as Google and Zimmer Biomet.

Kitware would like to congratulate and express appreciation to all of the employees who have helped its Carrboro office grow and succeed. They have made Kitware an even better place at which to work and have contributed significantly to open-source and scientific computing software. Kitware would also like to recognize the management of the Carr Mill Mall for its support of the office renovation.

Kitware Fuels Project for Planning Pediatric Surgery

Kitware announced a Phase II award from the National Institutes of Health to help surgeons plan and evaluate treatment for craniosynostosis. Craniosynostosis is a medical condition in which cranial sutures prematurely fuse during prenatal development. The resulting deformations can cause elevated intracranial pressure, brain growth impairment, and developmental deficiency in pediatric patients.

“Surgeons face tough decisions in treating craniosynostosis,” said Andinet Enquobahrie, Ph.D., MBA, a principal investigator on the project and the assistant director of medical computing at Kitware. “While the condition can inflict blindness, decrease motor skills, and reduce cognitive function, treatment options are often invasive and present risks such as blood loss. Currently, methods for planning and evaluating treatment are subjective and fail to adequately account for potential variations in patient anatomy.”

To provide surgeons with an objective and reproducible solution, a team from Kitware and Children’s National Health System is developing an intelligent cranial surgical planning system, known as iCSPlan. Unlike other systems, which base treatment plans on average cranial shapes, iCSPlan measures each patient’s cranium and compares it to over 300 computed tomography (CT) scans of crania without synostosis. Based on statistical analysis, iCSPlan determines the ideal cranial shape.

“The Phase I proof-of-concept study successfully achieved its aims and provided a solid understanding of the challenges and opportunities of cranial vault remodeling,” said Marius George Linguraru, Ph.D., a principal investigator on the project from the Sheikh Zayed Institute for Pediatric Surgical Innovation at Children’s National. “In the Phase II effort, we will improve iCSPlan and conduct a clinical feasibility study at Children’s National under the supervision of Division Chief, Plastic and Reconstructive Surgery, Gary Rogers, M.D.”

To assist surgeons in evaluating treatment options, iCSPlan generates quantitative and anatomically segmented cranial maps using modules from 3D Slicer. The team will extend iCSPlan to create additional visualizations that will interactively guide surgeons in virtually repositioning crania.

“3D Slicer is an open-source medical imaging application and a powerful resource for rapidly prototyping surgical planning software,” Enquobahrie said. “Its flexible architecture has allowed us to create an intuitive interface for iCSPlan.”

The team will enable iCSPlan to complete two additional tasks. The first is to analyze postoperative three-dimensional photography data, the collection of which does not expose patients to harmful radiation. The second is to account for any brain development that occurs in the period between diagnosis and postoperative data collection.

Research reported in this publication was supported by the Eunice Kennedy Shriver National Institute Of Child Health & Human Development of the National Institutes of Health under Award Number R42HD081712. The content is solely the responsibility of the authors and does not represent the official views of the National Institutes of Health.

Team Members Donate School Supplies to YMCA Program

Kitware collected school supplies at its headquarters in Clifton Park, New York, for the Southern Saratoga YMCA Running Start program. The Kitware Gives Back team worked with Kelly Mariano from the Southern Saratoga YMCA, who coordinates the program.

The program helps children from families with financial difficulties. The program aims to give participants backpacks with the supplies they need to start the new school year on the right foot. To identify eligible participants for the program, the Southern Saratoga YMCA works with the Shenendehowa school district.

Research Project Aims to Accelerate Multiphysics

Kitware has embarked on Phase II of a Department of Energy (DOE) Small Business Innovation Research project to help scientists study the multiphysics nature of particle accelerators.

“Scientists use particle accelerators in a wide variety of applications including research in pharmaceuticals, electronic materials and clean energy,” said Bob O’Bara, an assistant director of scientific computing at Kitware and the principal investigator on the project. “While scientists realize the importance of accelerators, they find that modeling accelerator systems raises issues of cost and complexity, as the process involves coupling multiple physics-based simulations such as thermal and structural simulations. Scientists currently lack effective computational tools to couple such simulations.”

Physics-based simulations often employ datasets that have several moving pieces such as models, meshes, and information that describes material properties as well as boundary conditions. Many existing technologies require scientists to manually track these pieces, which can lead to errors. For the DOE project, Kitware is working with collaborators to extend ModelBuilder, an application that automatically tracks data and guides it through the simulation life cycle.

“A major advantage of ModelBuilder is that it provides an intuitive way to set simulation input parameters,” O’Bara said. “ModelBuilder also offers a straightforward user interface, and it integrates with desktop, high-performance computing and cloud-based systems. As a result, scientists can test their designs for particle accelerators in a simple and cost-effective manner.”

O’Bara and his team are currently working to optimize a prototype of ModelBuilder that they created during Phase I of the DOE project. The prototype includes key capabilities for rendering and post-processing data, maintains a modular design and builds on the framework of Computational Model Builder (CMB).

“The CMB framework makes ModelBuilder highly customizable,” O’Bara said. “Scientists can seamlessly extend code or add plug-ins. Thus, the framework allows the utility of ModelBuilder to reach far beyond multiphysics to fields such as hydrology and nuclear energy.”

During Phase II, the team looks to add functionality for in situ analysis to ModelBuilder as well as support for workflow wizards and new visualization pipelines. At the end of the effort, the team will release the developed software as open source.

This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Acquisition and Assistance, under Award Number DE‐SC0013884.

This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.

VTK books Become Available for Download

On the website for the Visualization Toolkit (VTK), Kitware released PDF versions of “The Visualization Toolkit: An Object-Oriented Approach to 3D Graphics” and “The VTK User’s Guide.” Moving forward, Kitware plans to write new versions of the books and to transfer the books to open repositories. To download the books, please visit http://www.vtk.org/vtk-textbook and http://www.vtk.org/vtk-users-guide.

Kitware Prepares SC16 Presentation on Record-Breaking In Situ Run

Kitware has scheduled two times, during which it will deliver a presentation that provides exclusive insight on the largest-known in situ simulation run at its booth (3437) at The International Conference for High Performance Computing, Networking, Storage and Analysis (SC16). The presentation times will begin on Monday, November 14, 2016, at 7:30 p.m. MDT and on Tuesday, November 15, 2016, at 11:00 a.m. MDT, respectively.

Kitware participated on a team that worked with collaborators to complete the run for a project earlier this year. As part of the project, the team aims to create an infrastructure that can execute algorithms that users write across in situ software implementations. The particular implementation that the team used for the largest-known in situ simulation run combined ParaView Catalyst and SENSEI.

“ParaView Catalyst provides a lightweight ParaView server library, and SENSEI offers an interface that transfers analysis code among in situ infrastructures,” said Andrew Bauer, Ph.D., the lead developer of ParaView Catalyst at Kitware. “ParaView Catalyst and SENSEI streamline the simulation pipeline. Together, they enabled us to complete a larger run than ever before.”

For the run, ParaView Catalyst and SENSEI computed the Parallel Hierarchic Adaptive Stabilized Transient Analysis (PHASTA) simulation code. The run employed a 6.3 billion-cell unstructured grid and used 32,768 out of 49,152 nodes on Mira, an IBM Blue Gene/Q supercomputer from Argonne Leadership Computing Facility at Argonne National Laboratory. With 1,048,576 Message Passing Interface (MPI) processes on over 500,000 cores, the run quadrupled the size of the previous largest-known in situ simulation run. While the previous run also computed PHASTA with ParaView Catalyst, it did not utilize SENSEI.

“With ParaView Catalyst, users can specify which visualization and analysis capabilities of ParaView they seek to implement,” Bauer said. “Now, with SENSEI, users can better leverage in situ infrastructures to reduce runtime.”

The total runtime for the simulation clocked in at 653 seconds. Of this total, the time for in situ computation comprised 13 percent. During SC16, Kitware will address how information gleaned from the simulation run guided the development community to update ParaView. With these updates, the team projects that the total runtime for the same simulation would now come to 601 seconds, and the time for in situ computation would reduce to 5.6 percent of the total.

The SC16 presentation will complement a paper that team members wrote with collaborators for the conference. The paper, “Performance Analysis, Design Considerations, and Applications of Extreme-scale In Situ Infrastructures,” reviews in situ computation and shares additional results of the largest-known in situ simulation run. As well as Bauer, authors on the paper include Utkarsh Ayachit, Earl P. N. Duque, Greg Eisenhauer, Nicola Ferrier, Junmin Gu, Kenneth E. Jansen, Burlen Loring, Zarija Lukic, Suresh Menon, Dmitriy Morozov, Patrick O’Leary, Reetesh Ranjan, Michel Rasquin, Christopher P. Stone, Venkat Vishwanath, Gunther H. Weber, Brad Whitlock, Matthew Wolf, K. John Wu, and E. Wes Bethel. Bethel will discuss the paper at the State-of-the-Practice: System Characterization and Design session at the conference. The session will take place on Thursday, November 17, 2016, from 4:00 p.m. to 4:30 p.m. MDT in room 355-D of the Salt Palace Convention Center.

To learn more about the largest-known in situ simulation run, SC16 attendees can visit the Kitware booth during the conference exhibition from November 14 to November 17, 2016. Along with the exhibition, Kitware will participate in a number of conference activities that highlight its technology and expertise in high-performance computing and visualization. For details on scheduled activities, please refer to the event listing on the Kitware blog. To set up a time to meet with Kitware team members at SC16, please email kitware(at)kitware.com.

This material is based upon work supported by the U.S. Department of Energy, Office of Science, under Award Number DE-SC0012387.

This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.

Kitware Welcomes and Congratulates Team Members

Jared Vicory
Vicory started a new position as a research and development engineer on the medical computing team. He came to Kitware in May 2016 as an intern.

Alexis Girault
Girault returned to Kitware full time. He previously worked as an intern in Carrboro, North Carolina.

Pierre Guilbert
Guilbert began his role as an engineer in Lyon, France. His knowledge includes C++, Python, OpenCV, Open GL, OpenMP, Qt, and Visual Studio.

Jérôme Coste
Coste joined Kitware as an intern in Lyon, France. He currently attends Université de Technologie de Compiègne.

Hina Shah
Shah joined the medical computing team in Carrboro, North Carolina. In previous positions, Shah developed algorithms, tools, and applications for medical imaging.

Mohit Tyagi
Tyagi came to the Carrboro office as a long-term intern. He received a doctorate in mechanical engineering from Rensselaer Polytechnic Institute in May 2016.

Lucie Macron
Macron transitioned to a full-time team member. As a student at École Supérieure de Chimie Physique Électronique de Lyon, she completed an internship at Kitware SAS earlier this year.

Ashleigh Smith
Smith filled the role of controller on the finance team. For prior efforts, she completed audits as well as internal control risk assessments. She also led training sessions on technical accounting.

Beatriz “Bea” Paniagua
Paniagua made the move to Kitware as part of the Carrboro office. Prior to joining Kitware, Bea was an assistant professor at the Neuro Imaging Research and Analysis Laboratories at the University of North Carolina at Chapel Hill, where she focused on computer-aided diagnosis of craniofacial dismorphology and craniofacial surgery planning.

Louis Amore
Amore became a full-time team member in Lyon, France. In March 2016, he commenced an internship at Kitware, while he pursued a graduate degree from Université Claude Bernard Lyon 1.

Kitware continues to seek talented, motivated, and creative individuals to develop and deliver cutting-edge software products and services. Kitware employees enjoy an award-winning work environment that empowers them to pursue their passions. In addition to an excellent work environment, Kitware offers comprehensive benefits including flexible hours; a computer hardware budget; health, vision, dental, and life insurance; short- and long-term disability insurance; immigration- and visa-processing services; a relocation bonus; tuition reimbursement; and a generous compensation plan.

For descriptions of available positions, please see http://jobs.kitware.com/opportunities.html.