Facilities, Equipment, and Other Resources
The Quantitative Light Imaging (QLI) Laboratory
The QLI Lab (http://light.ece.uiuc.edu/), directed by Prof. Gabriel Popescu, is located in the Beckman Institute for Advanced Science and Technology at UIUC. The laboratory has office space for ten graduate students and two postdocs, with state of the art computers and network connectivity.
The QLI Lab has developed several novel imaging instruments (2 patents issued, 9 patents pending), which are currently in use, as follows
- SLIM- Spatial Light Interference Microscopy: provides nanometer scale structure and dynamics information about cells and tissues
- SLIT- Spatial Light Interference Tomography: provides full 3D images of cells and tissues
- iSLIM- Instantaneous SLIM: provides single-shot and 3-color SLIM images for fast and spectroscopic measurements
- Fourier transform light scattering: provides ultrasensitive static and dynamic light scattering from inhomogeneous media
- Dynamic scattering microscope: high-throughput cell microrheology
- Jones phase microscope: provides spatially-resolved Jones matrices of transparent and anisotropic samples
- DPM-Diffraction Phase Microscopy: provides quantitative phase image with sub-nanometer path-length stability. Suitable for biomedical applications in transmission mode and for material science applications in reflection mode
- wDPM- White Light Diffraction Phase Microscopy: DPM utilizing low-coherence white light source that diminishes speckles
- LFM- Laplace Field Microscopy: provides derivatives of the image field optically.
- prLCI– Phase-resolved low-coherence interferometry: provides rheological information on different samples.
QLI has two large laboratory rooms, 1,300 sq. ft. newly renovated space ideally suited for biomedical optics experiments. The QLI Lab is equipped with state of the art equipment, including:
- Four optical tables with air floating (10 and 12 foot)
- Two Axio Observer Z1 motorized inverted microscope (Zeiss) for epi-fluorescence, DIC, phase contrast, bright field imaging
- Axio Observer Z2 motorized upright microscope (Zeiss) for epi-fluorescence, DIC, phase contrast, bright field imaging
- Axiovert 200 motorized inverted microscope (Zeiss) for epi-fluorescence, DIC, phase contrast, bright field imaging
- Axiovert 200M motorized inverted microscope (Zeiss) for epi-fluorescence, DIC, phase contrast, bright field imaging
- IX-70 motorized inverted microscope (Olympus) for epi-fluorescence, DIC, phase contrast, bright field imaging
- SS1325 Swept laser source (Thorlabs) for low-coherence interferometry
- 4 computerized nanometer xyz stages
- various laser sources (laser diodes, doubled Nd:YAG, HeNe, etc)
- Two AxioCam MR B/W CCD (Zeiss)
- AxioCam MRc color CCD (Zeiss)
- Electron-multiplier CCD (EMCCD, Princeton Instruments)
- iXonEM+ electron-multiplier CCD (EMCCD, Andor)
- Neo sCMOS (Andor)
- Two ORCA-ER B/W CCD(Hamamatsu)
- ORCA-flash 2.8 sCMOS (Hamamatsu)
- megapixel video cameras (PAXcam)
- CARV spinning-disk confocal microscopy system
- 500MHz A/D acquisition board
- phase-only spatial light modulator (Boulder Nonlinear); 60Hz and 200Hz models
- phase-only spatial light modulator (Hamamatsu), optically activated
- amplitude liquid crystal spatial light modulators
- TC5000 Inverted Biological Microscope (Meiji)
- fiber optics components
- full range of opto-mechanic components
- double quad core PC server and other computers
The lab has in-house wet lab space:
- 2 incubators
- 2 biosafety hoods
- 4 refrigerators
- large counter top space for specimen preparation in each laboratory room
In addition, cell culture and autoclaving facilities are available in the building.
The QLI Lab is part of the Biological Intelligence Research Initiative, the Bioimaging Science and Technology research group at the Beckman institute, which offers an interactive and interdisciplinary environment for performing research at the highest level.
The Imaging Technology Group (ITG) is part of the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign (UIUC). As a core component of a major research institute at a large university, ITG has access to a complete support infrastructure. The various components are briefly described below.
Beckman Institute for Advanced Science and Technology
The Beckman Institute is an inter- and multidisciplinary research institute on the campus of UIUC. Devoted to basic research in the physical sciences, computation, engineering, biology, behavior, and cognition, it is organized around three main research thrusts: Biological Intelligence, Human-Computer Intelligent Interaction, and Molecular and Electronic Nanostructures. More than 600 researchers from 30 UIUC departments as far ranging as psychology, biochemistry, and industrial design work within and across these overlapping areas. The 180,000 square foot building was designed to foster collaborative research and features a wealth of open meeting spaces in addition to its state-of-the-art laboratories and over 200 offices. Support resources include an in-house networking group and a building operations staff (electrician, carpenter, plumber, HVAC).
Imaging Technology Group
Serving almost 700 researchers from the Beckman Institute and 68 departments on the UIUC campus, the Imaging Technology Group (ITG) provides two service facilities: the Microscopy Suite, and the Visualization, Media and Imaging Laboratory. These core facilities are open to all students, faculty, and staff at UIUC, as well as industrial users and independent researchers. Facility users are supported by a professional staff that includes PhD-educated microscopists, instrument technicians, visualization, graphics, and image analysis experts, and systems engineers, as well as graduate and undergraduate assistants. These staff have made ITG well known at UIUC as the place to go in order to solve the most difficult imaging needs.
A secondary focus of the group is to develop advanced imaging technologies, with emphases on projects in remote and virtual scientific instrumentation and their applications to science education outreach. This focus has led to their development and operation of two established and well-known educational outreach programs: Bugscope (http://bugscope.beckman.uiuc.edu), and the Virtual Microscope (http://virtual.itg.uiuc.edu). These programs provide scientific outreach to school children nationwide, and serve as a vehicle for bringing the research of UIUC faculty into the classroom.
The Microscopy suite provides high-end microscopy resources to ITG’s user base. A wide range of imaging modalities and supporting equipment is available for sample preparation and imaging. Instruments in the facility include state of the art light microscopes (dissecting, stereology, fluorescence, laser scanning confocal with two-photon and multiphoton, a second laser scanning confocal, reflected light with UV and Vis spectrometers), electron microscopes (environmental scanning [ESEM] with light-element EDS), transmission (TEM), scanning tunneling (STM) in the TEM) and scanning probe microscopes (atomic force [AFM], STM, and nearfield scanning optical [NSOM]). A wet lab is available for specimen preparation. Ancillary equipment includes an ultramicrotome, carbon evaporator, osmium vapor deposition system, sputter coater, fiberoptic puller, and dual-metal evaporator, as well as two particle-sizing systems, one of which is also capable of zeta potential measurements. The Microscopy Suite is supported by the entire staff of the ITG, and full-time staff include experts in light, electron, and scanning probe microscopies.
Visualization, Media and Imaging Laboratory
The Visualization, Media and Imaging Laboratory (VMIL) is a computer-based facility designed to support the computational needs of ITG’s users. Its resources include instrumentation for data capture, including 2D (high-resolution, optically accurate scanners for film, histology slides, and other materials; digital still SLR and quasi-SLR cameras; HD/SD digital and analog professional video cameras for capturing time-variant data) and 3D (contact- and optics-based 3D scanners for capturing the surface shape and texture of physical objects). The video production facilities include new HD-capable editing systems, providing scientists with the ability to acquire, process, record, and create both digital and analog video and audio. High-end workstations (Intel or AMD multi-core/64-bit with 4GB+ RAM, fast 3D graphics, striped RAID local online storage, etc.) running Windows XP, Mac OS X, and Linux support a wealth of software resources for 2D quantitative image analysis, volumetric data analysis, molecular simulation, data visualization, 3D modeling/animation, and scientific computing. Output options include standard 2D (high-quality photo and poster printing), as well as 3D (using a color-capable 3D “printer” (rapid prototyping device) to print physical objects from digital models). The VMIL is supported by a full-time manager to train and work with users in the facility. This consultant is backed up by an expert staff, who consult and provide services in various areas, including animation, still image production, image processing, video production, data conversion, research presentation, programming, and visualization.
Major Equipment in the ITG Facilities
- FEI Philips XL30 ESEM-FEG with Peltier stage, 1000 C and 1500 C hotstages, most other options
- Philips CM200 200kV TEM with standard, high-tilt, STM tip, Nanofactory STM, and strain holders, as well as cryo EM capability (w/cryoholder)
- Digital Instruments Nanoscope IIIa Multimode AFM with STM had
- Digital Instruments Bioscope AFM
- Custom-Built NSOM
- Leica SP2 Confocal Microscope with two-photon, multiphoton capability (materials)
- Leica SP2 Confocal Microscope (biology)
- Zeiss Dissecting Microscope
- Zeiss Fluorescence Microscope
- Stereology Workstation with StereoInvestigator and Neuolucida software
- Reflected Light Microscope with IR Camera and UV/Vis spectrometers
- Skyscan 1172 Micro-CT (5mm resolution) with stress/strain and micro-positioning stages
- 2D Image Analysis
- o MCID, Image Pro Plus, Fovea Pro.Optipix Photoshop Plug-ins, NIH ImageJ
- 3D Image Analysis
- o Amira/ResolveRT, Openlab, Volocity, VTK
- 3D Simulation and Scientific Computing
- o COMSOL Multiphysics, OpenDX, MATLAB, SPSS, SAS, Mathematica
- 3D CAD/Modelling/Animation
- o Maya, Rhinoceros 3D, AutoCAD, 3D studio, Solid Edge, Interchange
- Molecular Simulation
- o CaChe, Accelrys, VMD PyMol
- Multimedia Production
- o Final Cut Studio, Avid Xpress DV, Adobe Production Studio and Creative Suite 2, Cleaner, Sorenson Squeeze, Sound Forge
- 18 dual-processor Windows XP, Mac OS X and Lunux workstations
- 3D Acquisition Devices
- o Eyetronics Shapecam Field-Capable 3D Scanner
- o Microscribe 3Dx Contact-Based 3D Digitizer
- ZCorp Z406 Color-Capable 3D Printers
- 2D Acquisition Devices
- o Epson Perfection V700 Photo 6400dpi Dual-Lens Flatbed Scanner
- o Epson Expressions 10000XL 4800dpi Wide-format Flatbed Scanner
- o Nikon ED 8000 4000dpi Film Scanner
- Digital Cameras
- o Canon EOS-1Ds 11MP SLR (Lenses: 200mm through 5x macro)
- o Sony DSC-R1 10.3MP Fixed Lens (120-24mm equivalent)
- o Nikon Coolpix P3 8MP Point & Shoot
- Video Cameras
- o Canon XL-H1 1920x1080i HD Professional Video Camera
- o Canon XL-1 SD Professional Video Camera
- o JVC JY-HD10 1280x720p HDV Camera
- Video Production Facilities
- o Acoustic Systems Sound Isolation Booths
- o Professional Video Decks (HD(1080i)/HDV/NTSC/PAL/Beta Digital & Analog)
- o Professional Audio Processing Equipment (Mackie, Aphex, Alesis, AKG, etc.)
- o Final Cut Pro Studio Editing System (Intel 3GHz, 8GB G5 Mac Pro)
ITG Systems Infrastructure:
- HP ProLiant DL385 Dual-Processor AMD Opteron Linux Fileserver with 4GB memory
- 16TB Excel Meridian Fiber Channel RAID-6 Storage on Fileserver
- HP ProLiant DL385 Dual-Processor AMD Opteron Linux Webserver with 4GB memory
- Supermicro 1U Dual-Processor AMD Opteron Linux backup Webserver with 4GB memory
- Custom Dual-Processor AMD Opteron Linux Projects Server with 8GB memory
- 12TB Excel Meridian SCSI RAID-6 Storage on Projects Server
- Supermicro 1U Dual-Processor AMD Opteron Windows Backup Server with 4GB memory
- Excel Meridian 4TB SCSI RAID Enclosure on Backup Server
- Overland Storage Neo 4100 LTO-2 24TB Robotic Tape Backup Library
- Overland Storage Neo 4100 LTO-3 48TB Robotic Tape Backup Library
- 8 x 1U Supermicro Dual-Processor AMD Opteron Windows Cluster Servers with 4GB memory
- Gigabit (30-80MB/sec) Networking Throughout
- 10 Gigabit Network upgrade forthcoming
- Internet2 Connectivity for special projects
The available computational environment is particularly suitable to ensure decisive progress for the proposed project. The Computational Multiscale Nanosystem (CMN) group at the Beckman Institute operates two clusters for code, based on advanced Intel XEON processors, with a total of 64 processing units. The clusters are adequate for code development and testing necessary for the proposed research. The Beckman Institute provides space, utility costs and cooling, as well as fast networking support for these facilities. Prof. Ravaioli is leader and Prof. Aluru one of the most active member of the CMN group and their students and post-docs share office space designed for close collaboration. Profs. Ravaioli and Aluru are also members of the Multiscale Simulation group, one of four research trusts supported by the Institute for Advanced Computing Applications and Technologies (IACAT), which is the umbrella organization of the National Center for Supercomputing Applications (NCSA), a national facility internationally known as a leader in high-performing computing for over two decades.
NCSA was established in 1986 as one of the original sites of the National Science Foundation’s Supercomputer Centers Program. It is supported by the state of Illinois, the University of Illinois, the National Science Foundation, and grants from other federal agencies. The center is part of the Illinois Institute for Advanced Computing Applications and Technologies. For more than 20 years, NCSA has been a leader in deploying robust high-performance computing resources and in working with research communities to develop new computing and software technologies.
The center focuses on:
- Developing and supporting powerful, reliable computing, data, and networking resources that enable researchers to solve demanding science and engineering problems. We develop and explore innovative architectures and techniques to accelerate scientific computing.
- Working with research communities to help them fully exploit the extraordinary resources available on the Internet (computing systems, data sources and stores, and tools) with cyberenvironments.
- Developing software, techniques, and tools to improve national cybersecurity and to help law enforcement better respond to cyberattacks.
- Providing insights into complex systems and sharing the thrill of scientific discovery with the broadest possible audience through artful visualizations of scientific phenomena.
- Preparing the next generation of scientists and engineers to effectively use computational tools and techniques.
NCSA continues to support user communities by offering the resources that are the foundations of advanced cyberinfrastructure. Current computational resources exceed 145 TF supported by over 1.3 PB of disk storage as part of the infrastructure. The systems are on an internal multi-10GigE network.
NCSA Service-Hosting Environment
NCSA is provisioning a VMWare-based virtual machine service environment that can support on-demand instantiation of computational services for development and scalability testing and can host community services such as portals and virtual observatories. This environment currently hosts software configuration management repositories, bug tracking software, and development wikis for internal projects and portals, workflow execution services, and custom “virtual watersheds” and problem focused data analysis and modeling environments for a wide range of external user groups. The environment currently includes a high-performance computing cluster with 26 2GHz XEON processors on 13 nodes with 2Gb of memory each, and 4.5 terabytes of RAID5 storage and two new dual quad-core 2.8 GHz XEON machines each with 32 GB of memory and 4 terabytes of storage. Internal funding is being used to significantly expand this infrastructure over the next 6 months.
In fall 2010, Prof. Ravaioli has assumed leadership of the Multiscale Simulation group which is recipient of a large computational allocation on the Teragrid resources, suitable for extremely demanding production runs a necessary for multiscale imaging problems. NCSA is in the process to complete “Blue Waters”, slated to be the largest and most powerful Peta-Scale parallel computer in the world, and it also maintains a large cloud computing systems called “Blue Wave”. The imaging computational applications proposed for this project scale particularly well on parallel processors, and are excellent candidates for implementation on Blue Waters and Blue Wave. IACAT and NCSA have amassed a unique wealth of expertise that will be readily accessible to aid in the optimization and in the efficient implementation of our algorithms.
Imaging Initiatives at the University of Illinois at Urbana-Champaign
The University of Illinois at Urbana-Champaign has a long and rich history of significant achievements in imaging, from the early developments of ultrasound imaging and its bioeffects, to the development of magnetic resonance imaging by the late Paul Lauterbur, who received the Nobel Prize in Medicine in 2003 for his work in establishing this technique. Within biomedical imaging, faculty strengths in MRI, ultrasound bioeffects and imaging, CT algorithms, and optics are numerous. Campus expertise in imaging science, computational image processing, and visualization are also widely represented, particularly with the National Center for Supercomputing Applications (NCSA) and the future capabilities with Blue Waters, an NSF-supported peta-scale computing facility for science and engineering applications. The Beckman Institute for Advanced Science and Technology houses and operates several related shared-user facilities including the Biomedical Imaging Center (BIC) and the Imaging Technology Group (ITG), which is composed of a Microscopy Suite and Visualization Laboratory, and the Illinois Simulator Laboratory (ISL). The ISL operates and advances state-of-the-art visualization technology such as the CUBE and CAVE, which are room-sized immersive imaging technologies that allow investigators to “step into” their three-dimensional image-based data to manipulate and comprehend its significance. More broadly is the large number of faculty across many units that do or could utilize advanced imaging techniques to further their research investigations.
In recognition of this potential impact, our campus has recently launched a Strategic Imaging Initiative, and the Beckman Institute has recently added a fourth Integrative Imaging research theme. Both of these efforts reflect the significant and potential impact that imaging has on our campus, building on the many successes and essential elements already in place. The Strategic Initiative on Imaging is an effort to build a campus-wide, collaborative, integrated community of faculty, researchers, and students in imaging science, imaging technology, and the application, use, and interpretation of images. The Integrative Imaging research theme at the Beckman Institute is dedicated to bringing together ideas, modalities, and people in imaging to foster the interdisciplinary discovery of fundamental principles in imaging science, new enabling technologies for the next generation of imaging instruments, and novel techniques for basic and translational research.
Collectively as a campus, we are interested in the science of imaging, how data can be collected, processed, assembled, and presented as an image, how it may be visualized, and how it may be interpreted. We are interested in imaging technology, the innovation, design, engineering, investigation, and optimization of imaging instruments and methods to translate the data into images. Finally, we are interested in the application of imaging for new methods, techniques, and tools to further research and fundamental discovery across all fields of inquiry.
In the two years, the Strategic Initiative on Imaging has supported and facilitated several NSF and NIH Instrumentation Grants, organized meetings to open the discussion among imaging faculty in the Beckman Institute, started the planning of a weekly Imaging Forum seminar series and an annual Workshop on imaging, and strengthened collaboration with Carle Foundation Hospital in Urbana, Illinois, and the University of Illinois in Chicago.
These efforts are led by Prof. Stephen Boppart, M.D., Ph.D., along with Dr. Marina Marjanovic as Program Administrator, and Darold Spillman as Program Administrative Assistant, all located at the Beckman Institute. The goal of these new imaging initiatives is to help coordinate faculty efforts across campus and leverage campus strengths to achieve national and international recognition and prominence for the University of Illinois. This infrastructure will be leveraged by the work proposed for this project, elevating awareness and facilitating dissemination of research results.