FACILITIES & OTHER RESOURCES

Updated: 1 September 2020

Fields Relevant for the Integrated Cellular Imaging Core (ICI) Users

INTEGRATED CELLULAR IMAGING CORE (ICI)

The Integrated Cellular Imaging Core (ICI), one of the Emory Integrated Core Facilities (EICF), is housed in four main locations within the central research and clinical area of Emory’s campus (Fig 1 a&b), the ICI hosts 19 microscopes and 4 workstations in approx. 1800 sq ft of scope room, wet space and bench space (Fig 1 c). Each location requires either keycard or physical key entry to ensure only ICI trained users have access to the equipment. Each location has available wet space for basic preparations, in addition to being located within close proximity to multiple lab spaces, allowing for easy access to researchers own preparation areas. We house 19 different microscopes ranging from basic widefield setups to the more advanced, cutting edge, and custom built. These include confocal, spinning disk, multiphoton, super-resolution (SIM and STED), and light sheet (including a 3i lattice light sheet and in house OpenSPIM), with 10 systems (including at least from each modality) equipped for live cell conditions.

Service: The ICI team assists researchers with fluorescence experiments from an extremely broad range of scientific areas, from physics and chemistry to basic biology and translational research. Services range from experimental education and consultations, assisting and advising on sample prep, to optimizing data acquisition and subsequent analyses. The ICI supports investigators from start to finish, from bench to publication, at any point that assistance is needed. While using the microscope is the central part of our process, we are keenly aware that pre- and post-acquisition are equally important and are strongly emphasized during consultations. We help mold scientific questions to the right microscope, data set and analysis, and ultimately to researchers’ answers.

Data Collection, Management, and Analysis: All microscope acquisition data is automatically synced each night to an Emory Library and Information Technology Services (LITS) server to ensure redundancy. Data analysis can then be performed on either user located machines or ICI workstation locations. We advise, assist, and train users with data access and quantitative analyses as required. In addition to standard analysis and 3D visualizations, we provide custom Fiji macros and plugins, Imaris XTensions, and video sequencing (see NoPhotonLeftBehind YouTube channel).

Education: ICI holds periodic educational seminars and journal clubs. To advance our educational mission beyond the walls, we have a range of bite-sized YouTube tutorials on simple data analyses for Fiji, CellProfiler and Imaris, viewed by over 150k views and approaching 600 subscribers.

ICI Technical Support Team:

Adam Marcus, PhD – ICI Scientific Director

Dr. Marcus is an Associate Professor in the Department of Hematology and Medical Oncology and Georgia Cancer Coalition Scholar. He also serves as the Associate Director for Basic Science and Shared Resources for the Winship Cancer Institute, Director of Graduate Studies for the Cancer Biology PhD program, and Scientific Director of the Integrated Cellular Imaging Core (ICI). His laboratory has been focused on the cell and molecular biology of lung cancer invasion for the last 14 years. In particular, investigating how cells invade into 3-D microenvironments using a combination of live cell imaging approaches, 3D models, and standard molecular biology. Dr. Marcus developed and applies an image-guided genomics technique termed spatiotemporal genomic and cellular analysis (SaGA), utilizing photoactivated cell-specific selection for probing the biology of phenotypically heterogenous cells within a larger cancer cell population. In addition, Dr. Marcus’ lab is focused on STEM based learning in Georgia schools. In this role, he co-directs a 5-year NIH-funded, K-12 STEM outreach program (citizensciencehd.com) to promote diversity in STEM. This establishes a unique Citizen Science based curriculum in Georgia schools and has a full evaluation and outcomes component.

Neil Anthony, PhD – ICI Core Director

Dr. Anthony is an Associate Scientist with the School of Medicine and reports directly to the Assistant Dean of Research and the oversight committee for the ICI. He has 14 years of experience with advanced fluorescence techniques, including a biophysics PhD focused on fluorescence fluctuation spectroscopy (FFS), time-correlated single photon counting (TCSPC), coupled with multiphoton microscopy. He has built hardware setups including optical tweezers, laser scanned two-photon microscopy, and selective plane illumination microscopy, in addition to programming hardware control and analysis interfaces. He has experience with multiple imaging specific software analysis packages (including Imaris, Volocity, CellProfiler, and Fiji) in addition to general programming and analysis software and languages (Matlab, IgorPro, Java, C, Python). During his time with the ICI core (starting as an imaging specialist in 2013) he has developed existing 2D and 3D media skills for educational, reporting, and advertising core elements (Photoshop, Illustrator, and Blender). In addition, he has spearheaded a YouTube channel specifically for training users in bitesized sections. This ‘flipped classroom’ approach allows users to digest concepts prior to trainings. This channel has successfully been applied to data analyses, with microscopy concepts and acquisition software control in progress. Dr. Anthony provides outreach to the local community in seminars on microscopy techniques and data acquisition/analysis, in addition to teaching introduction classes for cancer biology and neuroscience graduate students.

Laura Fox-Goharioon – ICI Director of Research Projects

Ms. Fox-Goharioon is the Associate Director of Research Projects and experienced microscopist with over 34 years of cell biology and imaging experience at Emory University at the Whitehead location. She has over 13 publications focused on cell biology and imaging and has taken courses in super-resolution imaging and advanced image analysis, including the Analytical and Quantitative Light Microscopy course in Woods Hole, MA. She joined ICI at its inception and directly oversees the day-to-day operations of six microscopes including live cell, confocal, super resolution and multiphoton imaging.

April Reedy, PhD – ICI Research Specialist

Dr. Reedy is an Assistant Scientist with the School of Medicine with 15 years of applied microscopy experience in genetics and molecular biology, developmental biology and model systems. In her PhD in genetics and molecular biology she made numerous discoveries into the pathophysiology of Duchenne’s Muscular Dystrophy (DMD) in C. elegans. She has advanced confocal experience applied to C. elegans and Drosophila, including electrophysiology-based calcium imaging and ratiometric ROS imaging. Dr. Reedy also has immunofluorescence, pathology-based immunohistochemistry, and immuno-EM and cryo-sectioning experience. In addition to her extensive applied microscopy experience, Dr. Reedy has become a huge resource to investigators regarding experimental design.

William Giang – ICI Research Specialist

Mr. Giang is an imaging scientist with extensive data analysis, Python programming, and IT skillsets who holds a B.S. in Physics. He has two astroparticle physics publications from his time with IceCube, a South Pole Neutrino Observatory, where he utilized high performance computing clusters. After moving to Atlanta, he transitioned into a bioimage analyst to develop reproducible workflows for an Emory Cell Biology lab. Since joining ICI in 2018, he’s used his intimate knowledge of photodetectors to optimize acquisition settings and plan imaging experiments, especially in the context of high-resolution live cell microscopy. He applies classical and machine/deep learning strategies for image processing and analysis. Currently, his main roles include operating the lattice light sheet microscope and image analysis while also helping with confocal and super-res microscopy.

Gaurav Joshi, PhD – ICI Research Specialist

Dr. Joshi is an Assistant Scientist with the School of Medicine with 15 years of applied microscopy experience in cell biology and immunology.  His graduate work was focused on studying the mechanism of silica toxicity to alveolar macrophages to understand the development of the lung disease silicosis. This work demonstrated the mechanism of phagolysosomal leakage, ROS generation and cell death in alveolar macrophages using various fluorescent probes. He has led various microscopy-based projects and mentored undergraduate students in advanced cell biology laboratory course. In his postdoctoral work at UConn and Harvard School of Public Health, he showed the conditions under which silica nanoparticles are not toxic, a finding important for using them for drug delivery, and regulation of apoptosis in the lungs during development. Dr. Joshi has used various imaging systems such as laser point scanning and spinning disk confocal, live cell imaging, and high content imaging systems for his research on cells and tissues derived from animals and patients leading to nine publications. In his current role at ICI, he operates, trains and helps users from various disciplines with SIM super-resolution microscopy, laser scanning confocal and two-photon microscopy to address questions pertaining to basic and translational biology as well as make meaning out of their data. He keeps up with the current literature and his interest in new and upcoming technologies has enabled him to help groups with spatial transcriptomics.