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CytoData Symposium 2022


Join us for the 7th annual CytoData meeting, which will bring together experts from all over the world to address the challenges in cell imaging and analysis. This year’s theme is “Data analysis and deep learning strategies for image-based profiling in cell biology.” We aim to feature new tools, applications of tools, and new discoveries to bring the image-based profiling community together.

Oct 17 - 20, 2022

Allen Institute, Seattle, WA


8:00AM PT

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About This Event

The seventh annual CytoData meeting, hosted by the Allen Institute for Cell Science, took place October 17-20, 2022 in Seattle, Washington.

Established in 2016, the annual CytoData meeting brings together experts from across the world to address the challenges in cell imaging and analysis. This year’s theme was “Data analysis and deep learning strategies for image-based profiling in cell biology.” Quantitative image analysis is an emerging field that is developing at a rapid pace, and new tools and methods can help accelerate the analysis, yet democratization and standardization is needed to keep at pace. We aim to feature new tools, applications of tools, and new discoveries to bring the image-based profiling community together.

This year’s meeting was held in-person and consisted of three components:

Event Overview

Monday, October 17: 1:00-5:00pm

Main Symposium
Tuesday, October 18: 9:00am-5:00pm

Wednesday, October 19: 9:00am-5:00pm
Thursday, October 20: 9:00am-2:00pm


Organizing Committees

CytoData 2022 Local Organizing Committee
– Kaitlyn Casimo, PhD, Allen Institute
– Gideon Dunster, PhD, Allen Institute for Cell Science
– Wilhelmina Giese, Allen Institute
– Nick Hawley, Allen Institute
– Susanne Rafelski, PhD, Allen Institute for Cell Science
– Theo Knijnenburg, PhD, Allen Institute for Cell Science

CytoData Society Committee

Main Symposium

This year’s symposium will gather experts on image-based profiling, including a keynote address by Dr. Emma Lundberg. After the presentations, we will host a poster session for community members to showcase their own work.

We ask those interested in presenting a poster to complete an application, as space is limited. Poster applicants will have the option to submit their abstract for a short talk. Final decisions on posters will be made in mid-September.

Below is the list of speakers for the symposium. Speaker bios, talk titles and abstracts will be added in the coming weeks.

– Emma Lundberg, PhD, Stanford University – Keynote Speaker
– Pedro Falé Ferreira, MSc, ETH Zürich
– Uri Manor, PhD, Salk Institute for Biological Studies
– Lucas Pelkmans, PhD, University of Zurich
– Susanne Rafelski, PhD, Allen Institute for Cell Science
– Ana Sanchez-Fernandez, MSc, Johannes Kepler University
– David Van Valen, MD, PhD, California Institute of Technology
– Assaf Zaritsky, MSc, PhD, Ben-Gurion University of the Negev

Workshop Information

Join us for an afternoon of sessions dedicated to image processing, analysis, cloud computing and data access. The field of cell imaging and image processing is rapidly evolving, and researchers are in constant need of new resources that can help them obtain, manage, and analyze large amounts of data. Finding the right fit can be labor intensive and costly, which is why this year at CytoData we hope to reduce that effort by providing a series of workshops featuring cutting edge tools and resources.

Workshops will include sessions from the following organizations:

  • Allen Institute for Cell Science: “Open-source tools and resources for image data analysis”

  • Amazon Web Services: “Machine learning using Kubeflow”

  • Chan Zuckerberg Initiative: “napari: a multidimensional image viewer and analysis platform for Python”

  • Zeiss: “Create deep learning models and data- and Image processing workflows using the Apeer platform and python packages created by Zeiss”

Hackathon Information

One of the hallmarks of CytoData is the hackathon, where participants self-select into teams and work together to accomplish a complex task that has been specially prepared for the event. This year, we are excited to continue this tradition by hosting a two-day event. Participants will be working with the hiPSC Single-Cell Image Dataset which is generated at the Allen Institute for Cell Science and contains multi-channel images of 200,000+ live cells in 3D, spanning 25 major cellular structuresA version of this data has been specially curated for this event.

While the specifics of the hackathon will be communicated on the morning of Day 1, we are excited to provide a space for participants to leverage cutting-edge Python-based tools, stretch their imaginations and push the bounds of cell biological image analysis. At the end of the event, each team will be given time to present their work and receive feedback.

The Allen Institute shares a commitment to open data for participants to continue development of ideas and share progress after the event concludes. The hackathon will be an incredibly valuable space for networking, and we hope it will be the beginning of unexpected and fruitful collaborations!

While there is no additional cost for the hackathon, space is limited. If you are interested in participating, we are asking each person to complete a short application and share their experience with various Python-based tools.

Science Programs at Allen Institute