Imaging Resources

The ǧƵ has historically been a center for innovation in microscopy and biological imaging. In 1953 MBL Distinguished Scientist Shinya Inoué confirmed the presence of dynamic spindle fibers in meiotic cells, using the polarized light microscope he designed and engineered. Robert Day Allen, who was a pioneer in electronic aided light microscopy and demonstrated the applicability of differential interference contrast (DIC microscopy) in biology and medicine at the ǧƵ in 1970s and called MBL his home for many years. Today, the ǧƵ continues to serve as a central location for innovation and training in microscopy. Microscope developers and companies bring their instruments to be tested to the limits by resident and visiting investigators and faculty from diverse disciplines during the Advanced Research Training Courses. Through its convening power the ǧƵ has fostered advancements in imaging technology.

Due to its longstanding prestigious history with imaging and its unique ability to encourage research collaborations without institutional boundaries, the ǧƵ launched an Imaging Innovation Initiative. This Initiative addresses the broadly recognized need for an interdisciplinary center fostering collaborations between institutions to advance biological imaging and associated data analysis that is critical for sustaining the pace of basic, translational, and clinical research. The Imaging Innovation Initiative allows researchers and students to push the boundaries of microscopy to answer some of the most challenging scientific questions.

Visit the Strategic Initiative webpage for more information on the ǧƵ’s Imaging Innovation Initiative. Below is more information on the innovative new microscopes in development at the ǧƵ.  

Microscope and Computer Equipment 

Research and Development Instruments 

The ǧƵ has received generous support for its imaging innovation initiative from some of the largest private funders of science in the country including the Howard Hughes Medical Institute (HHMI), the Gordon and Betty Moore Foundation, the Arnold and Mabel Beckman Foundation, and the Chan Zuckerberg Initiative (CZI).  With these investments, the ǧƵ team is developing a wide range of cutting-edge microscope systems to meet our constantly growing imaging needs. In the last couple years, we have developed four systems which are being used by scientists and two additional systems are under development. There will be a constant pipeline of these innovative microscopes that transition from development to the ǧƵ’s Central Microscopy Facility.

With continuing multi-year NIH support, MBL Resident Faculty and Senior Scientists Rudolf Oldenburg and Michael Shribak developed advanced label-free quantitative imaging techniques, which are based on light polarization. All techniques are patented. The new techniques are implemented as add-on modules, which extend the possibilities of commercial research microscopes. ǧƵ fabricates these modules to other researchers upon request. Below are additional details on their instruments and contact information for potential collaborations.  

The Shribak Laboratory has devised two mutually complementary label-free methods: quantitative orientation-independent differential interference contrast (OI-DIC) and polychromatic polarizing microscopy (PPM). The OI-DIC generates quantitative phase image with the highest resolution. The uniqueness of PPM is that only it allows to visualize the birefringence instantly and independently on the specimen orientation. The PPM produces the color polarization images of low birefringent specimen with retardance from 1 to 200nm, which was not possible before. In image the hue represents orientation of slow axis, and the saturation depicts retardance amount. The PPM can be combined with a phase contrast (PhC) objective lens. The combined PPM/PhC image shows a visual scene, where the brightness corresponds to refractive index, and hue and saturation represent birefringence. The combined phase/ polarization image is impossible to obtain in any way, except with PPM.

The Oldenbourg Laboratory continues the development of polarized light microscopy techniques as a label-free imaging tool to study the structural dynamics of cell function. The lab maintains the website and OPS Resource at MBL, which provides instrumentation and operational support for advanced polarized light microscopy techniques to laboratories around the world. The lab’s current research interest lies in augmenting polarized light microscopy to the third dimension using advanced instrumentation and image processing algorithms to reveal the architectural dynamics in living cells in full 3D.

Central Microscopy Facility 

The Central Microscopy Facility (CMF) provides access to imaging instrumentation (microscopes) and image analysis and processing stations for the many research and educational components of the ǧƵ. The CMF maintains commercially available systems, some owned by the ǧƵ and some on loan, and some maturely developed custom instruments. The facility’s staff provide consultation on experimental design based on the instrumentation available, instruction on the operation of the instruments, and, when possible, technician-level operation. Usage is on an hourly fee basis with the goal of having research and education course staff operating the instruments whenever possible. 

Director Imaging Services; Staff Scientist: Louie Kerr (lkerr@mbl.edu) 
Associate Director of Imaging Services and Imaging Scholar: Carsten Wolff (cwolff@mbl.edu) 

Laboratory Operations Equipment 

The ǧƵ’s Laboratory Operations Department provides support for a wide variety of scientific equipment including microscopes and accessories. More information on the equipment and support for imaging-related courses and research can be found below and on the Laboratory Operations webpage.  

Vendor Equipment 

In addition to the in-house imaging equipment and resources, the ǧƵ receives instruments on loan and in-kind donations of products from over 150 companies. These vendors recognize the impact and benefit of providing cutting-edge, often pre-commercial equipment to MBL for its research and educational courses each year, with opportunities to collaborate, innovate and receive feedback directly from users while gaining exposure to a broader customer base. Company engineers and scientists collaborate with faculty and researchers, teach in courses, and assist students and research fellows. The program provides a win-win for commercial partners in exposing their brands and products to leading faculty and students from around the world and aiding in the research and development process. 

Conferences and Training 

Advanced Research Training Imaging and Computation Courses 

Almost all of the ǧƵ’s Advanced Research Training courses take advantage of its imaging capabilities but below are three courses specifically focused on imaging.  

The ǧƵ’s Division of Education hosts more than 20 Advanced Research Training Courses each year to train graduate students, postdoctoral researchers, and early-career researchers in advanced scientific techniques. Several courses listed below focus specifically on imaging and image analysis techniques, exposing the next generation of scientists to instrumentation and resources not commonly found at their home institutions.  

Analytical and Quantitative Light Microscopy: This 10-day course occurs annually and provides a comprehensive overview on the theory of image formation and application of video and digital methods for exploring subtle interactions between light and the specimen. The course is open to students and researchers from a wide range of backgrounds including biology, medicine, and material sciences.

Optical Microscopy and Imaging in the Biomedical Sciences: This course, which takes place over 9 days each summer, is designed primarily for research scientists, postdoctoral trainees, core facility directors/staff, and graduate students working in the biological sciences. The course provides an interactive, hands-on introduction to microscopy, digital imaging, and data interpretation. The course is designed to help students understand how to choose the right tool or instrument to address their own research questions. 

AI@MBL: Machine Learning for Microscopy Image Analysis: A new workshop held for the first time in May 2019 introduced advanced graduate students and postdoctoral fellows to deep learning analysis techniques. This course places deep learning in the broader context of computational imaging and machine learning. Students leave the workshop with an appreciation for the power and limitations of deep learning as well as knowledge of the key tools needed to apply deep learning methodology to their own research. 

The Analytical and Quantitative Light Microscopy and Optical Microscopy and Imaging in the Biomedical sciences courses were created in 1980 by Shinya Inoué and Robert Day Allen. Since the introduction of these two courses, new methods of microscopy and imaging have been invented necessitating new courses such as the Light-Sheet Fluorescence Microscopy Conference and Workshop described below.

Light-Sheet Fluorescence Microscopy Conference and Workshop

In 2021, the ǧƵ launched a new annual Light-Sheet Fluorescence Microscopy Conference and workshop aimed to bring together innovators in microscopy from academic institutes, industry, and federal laboratories to share and brainstorm the latest developments taking place in light-sheet research and its biological applications. A 3-day hands-on workshop will follow the conference for participants interested in gaining in-depth knowledge and experience about various light sheet microscopes. 

Undergraduate and High School Courses  

Many of the ǧƵ’s Undergraduate courses take great advantage of our imaging capabilities. The two undergraduate courses below specifically focus on imaging.  

For more information on any of the ǧƵ’s educational courses or to explore holding a course at the ǧƵ please visit the MBL Education webpage or contact education@mbl.edu.  

University of Chicago Courses 

  • Optics, Waves, and Modern Physics, taught by MBL's Rudolf Oldenbourg and UChicago's Patrick La Riviere and Ken Bader 
  • Imaging for Biological Research, developed by MBL Director Nipam Patel and taught by Louis Kerr and Carsten Wolff

High School Courses 

While we do not currently have a High School course specifically designed on imaging the three courses below introduce students to modern imaging methods including confocal microscopy and computational tools for visualization. View more information on other MBL High School courses.  

  • Anatomy & Physiology of Aquatic Animals, taught by MBL Veterinarian Lisa Abbo and Carrie Albertin
  • CRISPR/Cas9 Genome Editing of Aquatic and Marine Organisms, taught by Carrie Albertin and Scott Bennett
  • “Coral Reefs in a Changing World”, taught by MBL Associate Scientist Loretta Roberson 

Image Analysis Training 

In addition to providing consultation and training on equipment in the Central Microscopy Facility, the ǧƵ hosts an Image Analysis Center that provides access to analysis and processing stations for the various research collaborators who come to the ǧƵ. In 2020, the ǧƵ launched its Image Analysis Laboratory to meet the computational needs for imaging and analysis. The Image Analysis Laboratory facilitates four high-end workstations and a GPU server to researchers and course students for data handling and analysis. Additionally, the Lab houses various commercial analysis software and custom designed software for image analysis. Contact microscopy@mbl.edu for more information.

Industry Training 

The ǧƵ is developing a new application-based course for industry professionals who are interested in learning more about specimen preparation and protocols. More information on this course is forthcoming. If you are interested in learning more about this course, then contact the ǧƵ’s Education Department at education@mbl.edu.