5 Imaging Scientists Share Insights

Collaborating with Researchers to Improve Imaging Tools

Over the past year, 17 CZI Imaging Scientists — engineers, physicists, mathematicians, computer scientists and biologists — have been working in imaging cores and centers across the U.S. to advance the research and tools necessary to understand and identify disease.

They have designed new workshops and courses, updated imaging core facility infrastructure, developed new instrumentation, increased imaging pipeline efficiencies and more. CZI’s Imaging Scientists have also actively learned from one another, visiting each other’s facilities to share learnings and best practices. Read more about what they’ve accomplished so far.

Making Microscopy Accessible

Caroline Magnain

CZI Imaging Scientist Caroline Magnain at Massachusetts General Hospital’s Athinoula A. Martinos Center for Biomedical Imaging.

Caroline Magnain is promoting microscopy to researchers in a wide range of fields at the Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital. As the person who leads operations at the High Resolution Optical Imaging Core (pictured below), she guides scientists on how to optimally use the Martinos Center’s state-of-the-art optical imaging facilities to pursue cutting-edge investigations — overseeing the experiment protocols and user training and advising on data processing, and offering solutions for data management. Caroline also organizes workshops for students, postdocs, and faculty interested in understanding and applying advanced optical microscopy techniques.

The Athinoula A. Martinos Center for Biomedical Imaging’s High Resolution Optical Imaging Core.

“My favorite part of working in the imaging field is collaborating with researchers from vastly different backgrounds — neuroanatomists, computer scientists and physicians to name a few — and helping to build bridges between these fields. I keep learning new things every day.” -Caroline Magnain

This year, Caroline created manuals for users of two-photon microscopes and other imaging instruments, explaining all the steps necessary to use the equipment. All documents are written to be understood by all users, regardless of their background and level of training.

Innovating Core Infrastructure

Anthony Santella

Sloan Kettering Institute for Cancer Research, Molecular Cytology Core.

Computer scientist Anthony Santella leads image analysis innovation efforts — incorporating and modifying cutting-edge open source image analysis software into workflows to serve researcher needs at the Sloan Kettering Institute for Cancer Research, Molecular Cytology Core. His work is vital because what researchers need is constantly changing, as is image analysis software, with advancements in open source development and the expansion of deep learning-based approaches.

“I see a big part of my role as a computer scientist in an imaging core as helping researchers and other core members sort through all these methods and software to find the much smaller set of solutions that are really worth investing in.” -Anthony Santella

This year, Anthony’s work has promoted the increased use of open source image analysis solutions for solving user problems. Tools include Trackmate, for tracking and quantitative time lapse expression tasks; and QuPath, for interactive expression and tasks related to colocalization, a technique in fluorescence microscopy to observe overlap between multiple colored labels.

Building Next Generation Instrumentation

Srigokul Upadhyayula

CZI Imaging Scientist Srigokul Upadhyayula working at the ABC, University of California, Berkeley.

Over the past few months, Srigokul Upadhyayula and his team have assembled the instrumentation, computing, networking, and storage infrastructure for the Advanced Bioimaging Center (ABC) at the University of California, Berkeley. The ABC is a global collaboration center that provides state-of-the-art and pre-commercial microscopy, along with the dedicated human and hardware resources equipped to handle tera- to petabyte scale projects.

The Advanced Bioimaging Center (ABC) at the University of California, Berkeley.

“We’re working to develop open source computational workflows to handle and extract biologically meaningful information from the explosive quantities of data produced by high-speed and high-resolution instrumentations.” -Srigokul Upadhyayula

Assembling the ABC was no small task — it required retrofitting their existing lab with the appropriate infrastructure to build and house two of the Multimodal Optical Scopes with Adaptive Imaging Correction (MOSAIC) instruments. The MOSAIC is a highly engineered system with several imaging modalities vital for visualizing and quantifying complex biological systems across the relevant space and time scales.

Broadening the Imaging Community

Michelle Itano

CZI Imaging Scientist Michelle S. Itano at the University of North Carolina, Chapel Hill, Neuroscience Microscopy Core.

Michelle Itano facilitates the growing collaboration between researchers and computing specialists to design and disseminate efficient bioimaging pipelines at the University of North Carolina Chapel Hill Neuroscience Microscopy Core. Over the last year, she has worked directly with experimental biologists in the design and analysis of experiments, including leading over 90 individual training sessions for new users on microscopes and analysis workstations.

A large image of a mouse brain allows scientists to study how cells interact across distances. This image is stained for nuclear DNA (blue), a protein called aggrecan (green), and neurons (magenta). Photo provided by Michelle Itano.

“The imaging field is constantly moving and pushing boundaries. I am amazed at how creative people are and how inclusive the field is to members from across different scientific backgrounds. In imaging, a project can include the contributions of theoretical physicists, physicians, and high school students — all working towards the same goal.” — Michelle Itano

Michelle also designed a new semester-long graduate course — a hands-on, laboratory-oriented course in light microscopy for researchers in biology, medicine, and materials science to learn imaging tools. Additionally, Michelle participated in a lab exchange experience with Dr. Claire M. Brown at McGill University for a week-long job shadowing visit focused on the operation and maintenance of an imaging core, and also hosted a two-day seminar with CZI Imaging Scientist Caterina Strambio-De-Castillia.

Simplifying Data Sharing

Caterina Strambio-De-Castillia

CZI Imaging Scientist Caterina Strambio-De-Castillia looks into a microscope at the University of Massachusetts Medical School.

In order to find treatments for complex diseases such as cancer, diabetes, and inflammation, scientists need a lot of data, including from multiple experimental designs utilizing several different techniques across disciplines and from multiple laboratories. Unfortunately, often scientists work primarily within the boundaries of individual laboratories, complicating the exchange of data and analysis methods. Caterina Strambio-De-Castillia, Imaging Scientist at the University of Massachusetts Medical School, is developing shared procedures and standards so scientists can easily exchange big data and combine them in shared repositories.

Image of open source software tool Micro-Meta App. The tool is used to expedite the laborious task of collecting all necessary metadata information to interpret and reproduce fluorescence microscopy data. Image provided by Caterina Strambio-De-Castillia.

To encourage the widespread community adoption of data provenance and quality control guidelines, Caterina and her team developed a set of tiered guidelines that scale with experimental purpose and complexity as well as Micro-Meta App, an open source software tool that facilitates the automated annotation of microscopy datasets. The app expedites procedures of image data documentation, making it easy for investigators to make decisions about the utility of specific datasets for addressing their specific questions.

“Biological systems are among the most complex ever encountered. In order to understand their intimate functioning, scientists must harness this complexity and make it understandable via predictive models. I am convinced these enormous challenges can only be addressed by multiple laboratories working collaboratively towards the same goal.” — Caterina Strambio-De-Castillia

Interested in being one of our Imaging Scientists? CZI is now inviting applications for a second round of funding. Learn more about our current Imaging Scientists grantees.



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