Advanced Scientific Computing

Building a Cross-Institutional Collaboratory for 3D Visualization in Technical Education and Training
M. McGuigan, R. Bennett, L. Statest, D. Stampf, BNL, and G. Fong, SUNY Alfred State College

This work builds upon the successes of a previous NSF ATE grant (DUE-0070910) [1]. Therein, two western New York colleges (Alfred State College (ASC) and Jamestown Community College (JCC) partnered with Brookhaven National Laboratory (BNL) in an informal consortium of students, teachers, and scientists focused on the transferal of a cutting-edge, three-dimensional (3D) visualization technology from BNL to the colleges' classrooms. The institutional participants for the current expanded project are the Computational Science Center and the Office of Educational Programs at Brookhaven National Laboratory, SUNY Alfred State College, Bergen Community College, SUNY Jamestown Community College, SUNY Nassau Community College, Rochester Institute of Technology, and SUNY Suffolk County Community College.

The objectives for the current expanded project [2] are: (1) provide students with technical and non-technical experiences not available at their home campuses; (2) update and reinvigorate participating faculty by providing professional development and research collaborations with BNL staff; (3) create 3D Visualization Theaters at the colleges to permit campus-wide involvement in project activities and results; (4) develop specific applications to promote use of the campus visualization facility within mainstream teaching; (5) provide students with an opportunity to collaboratively design and deliver a course focused on training interested campus clientele in the use of the Visualization Theater, thereby providing both a means to disseminate use of the facility on campus and to enhance students' communication skills and curriculum-specific competencies.

In the first year of this two-year project 18 students from the six campuses worked on nine projects, as developed by the participating faculty members of each college. Two of these projects are discussed here in detail.

PyMOL Made EZ
L. Grell, C. Parkin, Prof. P. Craig, Rochester Institute of Technology, and L. Slatest, BNL

PyMOL [3] is a molecular modeling program that can be used in a wide range of studies within the scientific community. Its ability to produce informative, detailed, stereoscopic images makes it a very powerful tool both in the laboratory and in the classroom. However, the PyMOL user interface is difficult to use, and the need for command line interactions is not user-friendly. Using tools from Python’s Tkinter and PMW toolkits, a tabbed graphical user interface (GUI) plugin called PyMOL Made EZ has been created. The GUI contains a series of buttons and entry fields that allow users to easily select given attributes of a molecule and make changes to it with the click of a button.

The PyMOL Made EZ GUI features a notebook style design with separate tabs to distinguish one section from another. Some of its features are: (1) easy to use menus and buttons for the selection and manipulation of molecules, (2) nine predefined molecular views that provide clear and meaningful representations, (3) four movie settings that highlight key molecular aspects, (4) a toggle between PyMOL’s normal-viewing and stereoscopic-viewing options, (5) one-click access to primary citation and sequence information, (6) a Chime/PyMOL command converter, and (7) the ability to hide PyMOL’s internal interface.



Figure 1.  Presets Tab in the PyMOL Made EZ.

Stereoscopic Imaging of Scanning Electron Micrographs
V. Hall, K. Maggio, T. Smith, Prof. S. Beck, Nassau Community College, and J. Spiletic, BNL

Scanning electron micrographs exhibit stereoscopic qualities due to the high depth of field inherent in the use of the scanning electron microscope (SEM). Using the program StereoPhoto Maker [4], selected micrographs, created with the SEM at Nassau Community College [5], are made viewable as stereoscopic images. A routine procedure has been developed that permits movement from trial-and-error to a method that yields consistent results. As in conventional photography, creation of a stereoscopic image using the SEM requires a left-eye and a right-eye image. SEM stage controls permit sample movement in the X and Y axes, 360 degree rotation, and a tilt of 90 degrees toward and 20 degrees away from the signal detector. Images were captured using successive 2.5 degree increments, horizontal and vertical shifting, and sample rotation. Since specimen rotation could not be measured directly, the SEM-generated scale bar was used to measure increments depending upon magnification. The resultant two-dimensional images were opened in StereoPhoto Maker and combined to form a stereoscopic image based on two micrographs of differing perspectives. In addition to the routine method of generating stereo pairs through sample tilting, other methods were also investigated. It was determined that lateral shifting does not allow for the production of a visually satisfying stereoscopic image. However, rotation produced stereoscopic images of equal quality to that of tilted samples. Correlations have been found between surface topography and the initial degree of tilt required.

The specimens shown in the images (Figure 2) possess characteristics that are desirable for stereoscopic viewing, such as, physical features of varying surface textures and heights, overlapping structures, and inherent depth. The fish gills specimen creates a quality stereoscopic image because of the overlapping nature of its structures. The structures present in both the foreground and background provide depth to the photo. The leaf is an example of a specimen with varying surface features. Present in the foreground of the photo are hairs and extensive veining. In the background, there are several visible stomates that add variation to the surface topography.

 

References

• [1] Fong, G. et al. A Two Year College Cooperative Applied Research Initiative for Faculty and Students in the Engineering and Science Technologies, NSF Proposal DUE 0070910 (1999).
• [2] http://www.itd.bnl.gov/visualization/nsf_ate
• [3] http://pymol.sourceforge.net
• [4] http://stereo.jpn.org/eng
• [5] http://www.sunynassau.edu/webpages/biology/becks.htm

Last Modified: January 31, 2008
Please forward all questions about this site to: Claire Lamberti