Imaging Scientists and Imaging Software Fellows

The imaging of molecules, cells, and tissues is central to biomedical research and clinical practice. Advancing microscopy tools will help drive breakthroughs in curing, preventing or managing disease. Read more.

Read more about our Imaging Scientists.

BIO

Martin C. Fischer is an associate research professor in chemistry and physics at Duke University, where he directs the newly established Advanced Light Imaging and Spectroscopy (ALIS) facility. He received his PhD in physics from the University of Texas at Austin, studying quantum transport of ultracold atoms in optical lattices. His current work explores novel optical spectroscopy and microscopy techniques for molecular 3D imaging in highly complex materials. Prior to his arrival to Duke in 2005, Fischer worked in the department of radiology at the University of Pennsylvania, performing research on laser microscopy in skin and on gas magnetic resonance imaging in lungs. He also worked at Bell Labs/Agere Systems in New Jersey, working on high-speed transmission in optical fiber networks.


PROJECT DESCRIPTION

The ever-increasing quality and quantity of data requires and drives advances in microscopy and data analysis techniques. Such highly sophisticated instruments are most often developed for research use, and while equivalent, user-friendly commercial instruments eventually make it to the market, they remain out of reach for a majority of potential users in the meantime. The newly established ALIS facility at Duke will develop state-of-the art, customizable microscopes and make them accessible to the broader research community. Applications span disciplines from traditional sciences to humanities, including cultural objects such as renaissance paintings. Some ALIS microscopes will study small samples at high rates, such as the real-time monitoring of developing fly larvae; while other microscopes enable studying large samples at slower rates, such as the distribution of genetically labeled cells in an entire mouse brain.

BIO

Holly Gibbs is a biomedical engineer at Texas A&M University who studied with Alvin Yeh and Arne Lekven during her doctoral work on multiphoton imaging of brain development in zebrafish. She is interested in developing accessible microscopy, labeling, visualization, and bioimage informatics tools for creating multi-scale models of the emergence of brain structure and function. She will be joining Kristen Maitland at the Microscopy and Imaging Center to assist other researchers in managing, collecting, and analyzing experimental data from a new light sheet microscope.


PROJECT DESCRIPTION

Light sheet microscopy is a high resolution and minimally invasive imaging technique ideal for capturing movies of biological processes in living specimens, or rapidly imaging large fixed tissues. As biologists and biomedical researchers work to progress our understanding of the fundamental processes underpinning life and how disease occurs when those processes are disrupted, it's important to enable them with the best imaging and image processing tools available to avoid bottlenecks. The Microscopy and Imaging Center at Texas A&M University is being equipped with a new light sheet microscope, and Holly will recruit, train, and assist new users, as well as develop custom software for image processing and visualization.

BIO

Dr. Innocent’s expertise is in the testing and diagnostics of customized microscopy instrumentation. Her journey in imaging started in graduate school at Cornell University, where her thesis focused on vesicular trafficking dynamics in fly synapses. She then finished a postdoc at Oxford University, where her research centered on the application of reversible-switchable fluorescent proteins for use in non-linear SIM. Routinely using, creating and customizing computational tools to better quantify images is why she enjoys explaining the fundamentals of nontraditional microscopy. As the Assistant Director of the Cellular Imaging Core and research associate at the Harvard Medical School, she consults on the relevant and unique light microscopy methods used in advanced imaging.


PROJECT DESCRIPTION

There needs to be a new prototype of what the standard service imaging core can be. Such facilities do not need to compete with cores devoted to custom instrumentation, nor must they solely rely on box-commercial systems. To achieve this prototype, Dr. Innocent will: 1) facilitate tight-knit collaborations between cores, researchers, and microscopy vendors; 2) hold structured microscopy and optics education courses introducing new research technology or approaches; and 3) recruit new talent into imaging core management. Lastly, for microscopy education to be best applied and pervasive, Dr. Innocent will facilitate the education of core staff scientists via inter-core collaborations and exchanges.

BIO

Dr. Itano is a cellular biophysicist, Assistant Professor of Cell Biology and Physiology and Director of the UNC Neuroscience Microscopy Core, where she develops and customizes state-of-the-art optical imaging and analysis applications for a wide range of scientific research. She utilizes innovative fluorescence microscopy methods—including super-resolution and simultaneous multi-plane imaging—to investigate how viruses, such as HIV-1, infect cells.


PROJECT DESCRIPTION

Dr. Itano collaborates with colleagues from across scientific disciplines to find the best way to apply new, powerful imaging techniques to a wide range of scientific questions. She serves as the main source of training and guidance on how to coordinate and design imaging acquisition and analysis experiments, and has developed relationships with hardware and software engineers by continuously upgrading and customizing the services offered by the Core. Dr. Itano is engaging actively in a growing collaboration between researchers and computing specialists to design and disseminate efficient bioimaging pipelines for large imaging data sets to directly catalyze research findings.

BIO

Abhishek Kumar is joining the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts as a CZI Imaging Scientist and MBL Investigator. Currently, he is an Assistant Research Scientist at the University of Maryland, College Park, and a Guest Researcher at the National Institute of Standards and Technology in Maryland. Abhishek completed his MS degree at the Indian Institute of Technology, Kanpur, India, and his PhD at University of Massachusetts, Lowell, in physics. Subsequently, he was a postdoctoral researcher at Yale Medical School and at the National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health in Maryland. Abhishek has been associated with the MBL since 2013 as a Whitman Center scientist, a participant in the Analytical and Quantitative Light Microscopy advanced training course, and a Grass Fellowship recipient in 2015.


PROJECT DESCRIPTION

Dr. Kumar develops optical microscopes that enable biological scientists to learn how molecules, cells, and organisms function. His goal is to innovate new imaging technologies at MBL that address an increasingly diverse set of biological questions, ranging from the development of new model systems, to the structure of microbial communities, to understanding how organisms adapt to ecological changes. At MBL, he will develop a light sheet microscope that can be used for live imaging of larger organisms and embryos, such as squid or fish, at higher speed and for longer time periods. Dr. Kumar will also catalyze collaborations among the hundreds of scientists, faculty, students, and industry experts who convene at MBL for research at the interface of biology, microscopy instrument development, and computational image analysis.

BIO

Scot C. Kuo is Director of the Microscope Facility at Johns Hopkins School of Medicine and Associate Professor of Biomedical Engineering and Cell Biology. While studying the mechanics and movement of cells, he pioneered the use of microscopic optical tweezers to measure molecular forces and invented new optical approaches measuring intracellular mechanics. He also teaches an annual course on digital image analysis and optical microscopy to graduate students. As part of the Microscope Facility, he continues to develop and customize high-resolution instrumentation, sample preparation, and imaging and software analysis to support a broad array of biomedical researchers.


PROJECT DESCRIPTION

Dr. Kuo’s project has two goals: (1) to help biologists apply the latest microscope technologies to their studies, harnessing potentially revolutionary resolution and speed that would not be approachable without high levels of technical assistance; and (2) to educate students at all career stages on the power and concepts of quantitative imaging, particularly its applications to biological and biomedical problems.

BIO

Caroline Magnain is a physicist at the Athinoula A. Martinos Center for Biomedical Imaging, a research institute of Massachusetts General Hospital, affiliated with Harvard Medical School. Throughout her career, she has applied optical imaging to various domains, from cultural heritage to biomedical science, and has developed acquisition systems, optical simulations, and image analysis software. In 2011, she joined the Martinos Center to initiate a collaboration between the Optics Division and the Laboratory for Computational Neuroimaging. She uses optical microscopy to image the postmortem human brain’s cellular and fiber organizations. Her work bridges the microscale, obtained by optical imaging and histology, and the macroscale, obtained by MRI—the clinical standard for brain imaging.


PROJECT DESCRIPTION

Dr. Magnain will provide imaging expertise to the research community at the Martinos Center and its extended network of collaborators. She will provide training for investigators to operate the microscopy core resources and assist with experimental design, image acquisition, and data analysis. Her guidance will help scientists utilize state-of-the-art imaging facilities to pursue cutting-edge investigations into compelling issues in medicine and physiology. She will also engage with biologists in broadly disseminating information about advanced optical imaging techniques—training students, postdocs, interns, and other researchers interested in advanced optical microscopy techniques; helping to organize and share data analysis software; and working with information technology teams to help shape decisions pertaining to developing new data-sharing resources to support the research community.

BIO

Dr. McArdle is a bioengineer with a passion for developing tools that will help accelerate biomedical research. She has experience in a variety of microscopy methods, as well as image analysis, hardware integration, and coding for automation. She joined the La Jolla Institute for Immunology microscopy core facility in 2015, where she collaborates with biologists to help solve their imaging challenges.


PROJECT DESCRIPTION

Dr. McArdle’s main focus is on making cutting-edge imaging and analysis methods accessible to non-expert biologists. She trains other scientists in new software and hardware, writes scripts for automated image processing, and performs intravital experiments. Recently, she has taken on establishing super-resolution imaging methods in the core facility to gain access to the highest level of detail of cellular structures.

BIO

Dr. Pécot is an engineer and applied mathematician with expertise in bioimage informatics. He has developed algorithms and analysis pipelines in the Icy suite of microscopy software for a variety of biological applications. Since he joined the Hollings Cancer Center at the Medical University of South Carolina in 2016, he has been developing a deep learning framework for segmenting cell nuclei in microscopic images, which is used in a pipeline designed to profile tumor immune status, among other applications.


PROJECT DESCRIPTION

Dr. Pécot teaches algorithms how to recognize objects in images, and his project aims to enable biologists to apply deep learning tools to their own images. Interacting with biologists allows him to identify the needs required to develop a deep learning suite for segmentation at a large scale. This suite will then be extended to design software that biologists can run themselves. Additionally, he teaches a bimonthly tutorial about free software used to process biomedical images.

BIO

Dr. Rowland has over 18 years of experience in biomedical imaging and six years in instrumentation for physics experiments. His specific focus was on the production, chemistry and characterization of non-standard PET radionuclides in the first years of work in biomedical imaging. From there, he transitioned to developing techniques for imaging small animals on microPET and microCT technologies. Since 2007, he has been responsible for collaborating with principal investigators on the design and implementation of imaging experiments on small animal in vivo imaging technologies, including MRI and PET. He also worked to establish a strong MRI and CT research program at CMGI, particularly in high resolution imaging for correlative microscopy.


PROJECT DESCRIPTION

Dr. Rowland works with instruments that allow for live animal imaging, similar to how people are scanned in the clinic, such as MRI, CT or PET scanners. These preclinical technologies are used to understand animal models for human disease. Scanners in CMGI, such as the CT and MRI scanners, are capable of assessing tissues down to the level of a few microns to tens of millimeters. Dr. Rowland will refine and optimize imaging protocols and software for these scanners to correlate with microscopy. He will also consult with scientists to identify their image analysis bottlenecks and needs, and work collaboratively to document unsolved image analysis challenges and communicate them to the wider imaging communities. Additionally, he will create instructional videos to cover basic and advanced image analysis approaches.

BIO

Anthony Santella is a computer scientist with a background in image and data analysis, computer vision, visualization, and graphics. Born in NYC, he completed a BA at New York University and PhD at Rutgers. He has 11 years of experience collaborating with biologists to develop practical, open source tools for challenging image and data analysis tasks, with a focus on long-term cell tracking in live fluorescence imaging. He is joining the Molecular Cytology Core to lead an image analysis innovation effort: developing, testing, deploying, and adapting cutting-edge open source image analysis software to serve researcher needs.


PROJECT DESCRIPTION

The Image Analysis Innovation program at Memorial Sloan Kettering’s Molecular Cytology Core ensures researcher access to cutting-edge image analysis software and techniques. The image analysis needs of researchers are constantly changing, as is image analysis software—particularly as open source development efforts proliferate and deep learning-based approaches become mainstream in science. Making trade-offs between competing algorithms and software packages and managing training data is as important as computing power. The innovation program provides dedicated computer science expertise to deploy novel solutions to the image analysis tasks of users and to train researchers in the fundamentals of image analysis.

BIO

Dr. Scott earned his PhD in biochemistry from South Dakota State University in 2015, working with Dr. Adam Hoppe. His graduate and postdoctoral research focused on the development and application of advanced microscopy methods investigating cellular dynamics, protein-protein interactions, image processing, and advanced analysis of microscopy data. He is a postdoctoral researcher in the BioSNTR imaging core, a team science center that includes biologists, microscopists, and computer scientists working together to develop gene-edited cell lines expressing fluorescent protein fusions to image molecular activities within living cells.


PROJECT DESCRIPTION

Dr. Scott will assume the role of Research Assistant Professor in Nanoscience and Nanoengineering at SDSMT, and will lead the development and application of the facility’s recently constructed lattice light sheet microscope, licensed under an agreement with Howard Hughes Medical Institute. He will be responsible for teaching users about instrumentation and experimental design, along with facilitating sample preparation, image acquisition, data processing, and quantitative analysis. He will also facilitate collaborations to explore the nuances of living cells and membrane dynamics and probe the genetic basis of cellular function.

BIO

Caterina Strambio-De-Castillia is a cell biologist with a primary interest in promoting scientific advances through distributing reproducible, well-documented datasets and analysis procedures. She learned her trade in the laboratory of Gunter Blobel, a pioneer of modern cell biology. After joining the Luban lab, she realized that better understanding of how HIV-1 traverses from the cytoplasm to the nucleus would require development of software tools and metadata standards, aiding cross-lab comparison of raw-image data, analytical results and procedures. Her passion is to develop microscopy and image analysis metadata standards to ensure state-of-the-art bioimaging techniques are available to bench scientists, regardless of their computational expertise.


PROJECT DESCRIPTION

The management and analysis of modern microscopy data pose enormous challenges due to lack of automation, standardization and documentation, often making it impossible for different laboratories to work together and hampering scientific progress. Caterina will address this gap by developing easy-to-use, shareable image-analysis pipelines designed to incorporate the automatic capture of data provenance information, quality control, and metadata standards. These pipelines will “stitch together” existing in-house software and popular open-source packages (e.g. OME, Fiji/ImageJ, CellProfiler, scikit-image), providing a bridge between individual laboratories and state-of-the-art global bio-image informatics development initiatives. Caterina will also organize courses and workshops to train experimental scientists to use this technology for their everyday work.

BIO

Dr. Taylor became interested in imaging during graduate school at Brown University while pursuing a PhD in neuroscience and using simple epifluorescence and confocal microscopy. He directed a light microscopy and small animal imaging core at Purdue University, where he became well-versed in the fields of imaging and image analysis. The excitement of super resolution and light sheet microscopy next drew him to the Janelia Research Campus Advanced Imaging Center, where he worked with visiting scientists on high-speed structured illumination microscopy and new image analysis approaches. As Managing Director of the BRCF Microscopy Core, he provides overall direction, engages students and faculty, and solves the core’s most challenging imaging problems.


PROJECT DESCRIPTION

Dr. Taylor plans to spend part of his time on education and outreach, which are critically important for any new imaging or analysis technology to be useful. He will also work collaboratively to develop new image acquisition and analysis strategies—including a new image compression method that aims to be lossless relative to relevant content—that will benefit core users. This method should achieve higher compression levels than are possible using common existing approaches that aim to preserve pixel intensities. He will also develop an image analysis-enabled acquisition method based on widely available hardware that can acquire volumetric fluorescence images of monolayer cell cultures as gently as state-of-art light sheet approaches when staining patterns are sparse.

BIO

Srigokul (Gokul) Upadhyayula’s research interests bridge applied engineering with basic science. He studied the charge transfer properties of cyanine dyes and bioinspired electrets using ultra-fast femtosecond spectroscopy as a doctoral student with Valentine Vullev at the University of California, Riverside. Gokul joined Tom Kirchhausen’s group at Harvard Medical School/Boston Children’s Hospital as a postdoctoral fellow, where he focused on questions addressed at a molecular level using lattice light-sheet microscopy (LLSM) with high temporal and spatial resolution. In parallel, Gokul joined Eric Betzig’s group at Janelia Research Campus as a visiting scientist, where he collaborated on the adaptive optical LLSM project to investigate sub-cellular dynamics within the natural environment of multicellular organisms such as zebrafish embryos, and on the expansion microscopy and LLSM project to image the entire fly brain and mouse cortical column with synaptic resolution. Gokul will join UC Berkeley as the scientific director for the Advanced BioImaging Center (ABC).


PROJECT DESCRIPTION

Dr. Upadhyayula, along with ABC co-founders Nobel Laureate Eric Betzig, Xavier Darzacq, Doug Koshland, and Robert Tjian, aims to bring scientists with broad specialties (instrumentation, biology, applied mathematics, and computer science) together and provide free access to advanced imaging systems and resources. To start, he is building two cutting-edge adaptive optical multi-functional microscopes to enable imaging across scales spanning several orders of magnitude in space (specimens up to several millimeters in size) and time (imaging sessions lasting multiple days). The ABC seeks to provide cutting-edge microscopy and dedicated human and hardware resources capable of handling tera- to petabyte scale projects, and to develop robust, open source computational workflows that allow scientists to extract biologically meaningful insights.

BIO

Dr. Waters has broad expertise with light microscopes, detectors, and image acquisition software, and a strong working knowledge of image analysis, processing, and data management. She has focused the majority of her career on educating research scientists on best practices in quantitative imaging. In addition to teaching microscopy in graduate program courses at Harvard, she has developed many educational resources for the greater imaging community, including an intensive two-week Cold Spring Harbor Laboratory course and the YouTube channel Microcourses. Dr. Waters also founded the Advanced Microscopy Post-Doctoral Fellowship Program at Harvard, which provides extensive training in microscopy and core facility management for those pursuing a career in imaging science.


PROJECT DESCRIPTION

Dr. Waters seeks to promote and support the imaging scientist career path, and to continue to develop tools and educational resources that help scientists perform rigorous quantitative microscopy experiments. She is developing the website Microlist.org, which collates resources for research scientists using microscopy and image analysis, including courses, meetings, educational materials and job opportunities. She also plans to create a short, intensive course for imaging scientists supporting biological research, which will include strategies for developing effective imaging lectures and laboratory exercises, methods of instrument quality control, and opportunities to enhance reproducibility of imaging research. She looks forward to advising the CZI team of software engineers on areas where they might help enhance the quality and reproducibility of imaging data.

BIO

Dr. Weber studied biotechnology, gained a PhD at the interface of biology and microscopy development, and did a postdoc and worked in light microscopy core facilities in the United States and Germany. Over the course of his career, he gained insights into state-of-the-art biomedical imaging from several perspectives and acquired expertise in integrating, using, and training both commercial and custom-built advanced light microscopy. He has contributed to workshops and courses, given lectures and presentations, and authored book chapters, reviews and peer-reviewed articles. He now works remotely as a Field Application Specialist for the Greater Boston Area.


PROJECT DESCRIPTION

Dr. Weber is developing the microscopes and infrastructure for a virtual imaging facility, where compact yet powerful light sheet microscopes (“Flamingos”) travel between research labs. His team will give every researcher access to custom high-end microscopy and use their feedback to modify and further improve these microscopes. This unique approach to sharing microscopy technology will improve collaboration and communication between biologists and microscopy developers.

Read more about our Imaging Software Fellows.

BIO

Allen Goodman, a Senior Software Engineer at the Broad Institute of MIT and Harvard, working in the lab of Anne Carpenter, will support the existing open-source CellProfiler codebase as part of contributing to collaborative, open-source projects that will benefit the entire bioimaging software ecosystem. Goodman will focus on the most important collaborative projects needed to transition the bioimaging software ecosystem towards the use of deep learning and web-based applications. This will include a web application for evaluating segmentation algorithms that help analyze images, training a deep learning model to robustly detect nuclei across experimental setups, and creating a deep learning-based tool to classify cell types. Goodman will also assess and improve integration between CellProfiler and other key bioimaging software libraries, such as scikit-image.


PROJECT DESCRIPTION

The open-source CellProfiler has been used in a wide range of experiments, analyzing images of specimens such as cells, yeast colonies, and worms in support of research on diseases ranging from breast cancer and leukemia, to liver disease and HIV. The software has been cited over 6,200 times since being published in October 2006.

BIO

Juan Nunez-Iglesias, a Bioimage Analysis Research Fellow at Monash University in Australia, will work to advance both the technical capabilities and community growth and mentorship around base software libraries for image analysis in Python. Juan will focus on developing scikit-image while also collaborating to improve the surrounding ecosystem, including NumPy and SciPy (the basis of scientific computing in Python), CellProfiler (a graphical user interface for cell-based measurements in images), and dask (a library for computing on very large datasets).


PROJECT DESCRIPTION

scikit-image is a community-driven Python project consisting of a collection of algorithms for image processing available free of charge and free of restriction. With over 285 contributing developers, and 14,000 packages that depend on it, scikit-image plays a critical role across many domains of science, ranging from biomedical image processing to astronomy, and many things in between.

BIO

Curtis T. Rueden, a Software Architect in the Eliceiri research group at the University of Wisconsin-Madison, will continue to develop ImageJ and Fiji in collaboration with several international partners. This includes expanding its contributions from non-programmers, amateur programmers, and professional developers alike. A concerted software engineering effort is needed to support emerging imaging paradigms and ensure Fiji’s ability to handle the requirements of modern science. Curtis will assist in this engineering effort and lead efforts for collaboration between tools and projects in the open-source imaging community.


PROJECT DESCRIPTION

ImageJ, an open-source Java program, was originally released in 1997 as a freeware image analysis program, and is one of the most-used tools for imaging scientists across the globe. ImageJ has a large audience of users and developers of varying skill levels, interests, and applications, and has since grown into the Fiji and ImageJ2 open-source platforms with over 1,000 plugins (and counting), which add key image analysis tools. ImageJ and related projects are cited in over 10,000 publications across a wide range of domains of biology.