The spirit of partnership at Stanford Bio-X continues throughout the Clark Center with specialized laboratories working to educate, to discover, and to disseminate the knowledge gained.
- Optogenetics Innovation Laboratory (OIL)
- National Center for Biomedical Computing (Simbios)
- Stanford Radiology 3D and Quantitative Imaging Lab (3DQ Lab)
- Stanford Center for Innovation in In-Vivo Imaging (SCI3)
- Microfluidics Foundry & Clean Room
- Clark Center Tissue Foundry
- Stanford Byers Center for Biodesign
- Leica SP8 Confocal Microscope
- Cryo-Electrom Microcscopy (CryoEM)
Optogenetics is an emerging field combining optics and genetics to probe neural circuits within intact mammals and other animals at the high speeds (millisecond-timescale) needed to understand brain information processing.
Fiber Photometry uses GECIs (genetically engineered calcium indicators) to measure calcium levels in the brain during behavior studies of live animals, allowing researchers to optically record in real-time natural, specific-connected neural activity.
The mission of the Optogenetics Innovation Laboratory (OIL) is to train scientists in Optogenetic techniques, with synergistic curriculum in fiber photometry and CLARITY in order to fundamentally advance the knowledge of neuroscience. In the last decade, more than 600 participants from Stanford and around the world have enrolled in training courses hosted by the OIL.
The lab is directed by Dr. Karl Deisseroth and is served by an Advisory Committee drawn from the Schools of Engineering, Humanities and Sciences, and Medicine. These core mission goals are being achieved with space, equipment, training, and tech support to the Stanford, national and international communities.
Directed by Scott Delp and run by Joy Ku, Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions.
Its mission is multi-fold:
- to perform high-quality research in simulation
- to develop infrastructure and disseminate tools, models, and data to facilitate the use of physics-based simulation
- to train biomedical computational scientists.
Simbios is focused on the physical reality of biological structures and provides a critical piece of a national biomedical computing infrastructure. The software programs produced by Simbios continues to make an impact on the scientific community. All three of these software packages are open-source and are available for download at http://simtk.org.
The Stanford Radiology 3D and Quantitative Imaging Lab (3DQ Lab) was established in 1996 with the goal of developing and translating innovative techniques into clinical practice for the efficient display and analysis of medical imaging data. This was motivated by a paradigm shift from cross-sectional to true volumetric imaging in several radiological imaging modalities, especially CT and MR.
The clinical arm of the lab processes over 1,100 patient cases per month and contains knowledge and resources that augment the innovative research being done in the Radiology Department as well as by Stanford Bio-X members. The 3DQ Lab is an excellent resource for medical professionals to obtain clinical training in 3DQ image post-processing and quantitative imaging methods. A variety of educational opportunities are available for Stanford medical affiliates as well as technologists, radiologists and imaging specialists from domestic and international medical imaging communities.
The mission of the Stanford Center for Innovation in In-Vivo Imaging (SCi3) is the application and advancement of technologies for in-vivo biological assessment and imaging in animal models. The instrumentation supports the development of reagents and approaches that will reveal in-vivo changes at the molecular and cellular level such that a greater understanding can be gained in animal models.
SCi3 provides state-of-art and first-of-its-kind preclinical imaging technologies to the Stanford research community, offering emission tomography (PET), magnetic resonance imaging (MRI), computed tomography (CT), magnetic particle imaging (MPI), optical imaging, and ultrasound and photoacoustic imaging. In 2019, personnel from 260 principal investigators' laboratories conducted over 11,000 hours of SCi3 imaging activity.
The Stanford Microfluidics Foundry is a shared-access Class 10,000 and Class 1,000 cleanroom facility located at the Clark Center. The mission of the Microfluidics Foundry is to provide Stanford students and researchers with the equipment and facilities to fabricate integrated microfluidic devices. This equipment includes a Karl Suss MA6 Mask Aligner and spin-coaters for photolithography, as well as a parylene coater, micro-profiler, and a system for oxygen plasma treatment.
The Stanford Microfluidics Foundry was founded in 2005 and is part of Professor Stephen Quake’s laboratory research group in the Bioengineering Department. The facility currently supports over 25 active users from 6 different research groups.
The Clark Center Tissue Foundry is led by Oscar J. Abilez, MD, PhD, an Instructor in Cardiovascular Medicine. His lab’s research interest is aimed at elucidating how various biophysical stimuli regulate cardiovascular development across time and length scales that span several orders of magnitude, primarily using human pluripotent stem cells as a model system. He collaborates with investigators both within and outside Stanford to provide his expertise and access to various experimental equipment and devices. Currently, research in the Clark Center Tissue Foundry focuses on applying optogenetic, biochemical, electrical, and mechanical stimulation to control and manipulate the directed differentiation, maturation, and organization of human pluripotent stem cell-derived cardiovascular cells and tissues. Guided by quantitative approaches, Dr. Abilez's long-term research goal is to ascertain the mechanisms by which various biophysical stimuli direct the development of engineered cardiovascular cells and tissues from human pluripotent stem cells, and to use these findings to address challenges in the basic, translational, and clinical sciences.
The Stanford Byers Center for Biodesign, a unit of the Stanford Bio-X initiative, is dedicated to developing world-class innovators who have the talent and ambition to create the next generation of advanced health technologies. Students and faculty are trained in the biodesign process, a proven, team-based approach to technology innovation that centers on identifying and characterizing important clinical needs as the essential first step in successful inventing.
A core offering of the program is a year-long Innovation Fellowship, a hands-on training program for selected graduate and postdoctoral students drawn from engineering, medicine, and business. In addition to the Innovation Fellowship, Biodesign offers graduate and undergraduate classes, an executive education program, and a Faculty Fellowship that introduces 12 engineering and medicine faculty members per year to technology invention and transfer. Stanford Biodesign also works closely with the Office of Technology Licensing, the Department of Bioengineering, and Spectrum (the Stanford Center for Clinical and Translational Research and Education) to provide mentoring and seed funding to accelerate the translation of faculty and student inventions into patient care.
Since its founding in 2001, Biodesign trainees have created 51 companies based on technologies invented during the program. To date, these new technologies have been used in the care of more than 3.4 million patients. An additional 28 faculty projects have received seed funding and mentoring from Biodesign that resulted in new company formation.
The Clark Center supports a Leica SP8 confocal microscope to provide super-resolution, high-speed imaging, and the capability to image multiple fluorescent markers simultaneously. This microscope offers simultaneous multicolor imaging in super-resolution down to 120 nm, live specimen imaging thanks to fast acquisition rates, and sample protection thanks to low phototoxicity.
Working with Drs. Brian Kobilka and Georgios Skiniotis, Stanford Bio-X has built a cryo-electron microscopy core at the Clark Center, to greatly improve imaging capacities and to allow researchers to investigate structural biology questions with unprecedented imaging resolution.