BioImage Informatics 2019

CytoData unites microscopists and researchers mining cell imaging data to define novel and unique ways to tackle challenges in image analysis.

Since 2016 CytoData events have proven incredibly exciting and we hope to replicate the virtues of this meeting once again in 2021! The meeting is composed of four sessions including Methods, Primary cells, Stem cells, and others, all featuring 10-minute talks. We have a fantastic line-up of invited speakers! As in 2020, CytoData is held virtually this year from Wednesday 13-Friday 15th October including the popular Hackathon in the afternoon.

Find out more about the CytoData Society and

BioImage Informatics 2019 is an annual meeting in the processing, analysis, and extraction of information and knowledge from biomedical images. This year's conference took place at the Allen Institute from October 2-4, 2019, and was organized by Mike Hawrylycz from the Allen Institute for Brain Science and Winfried Wiegraebe from the Allen Institute for Cell Science. 

Advances in biological cell and tissue labeling and automated microscopy and imaging have revolutionized how biologists visualize molecular, cellular, and compartmental structures and study their respective functions. Huge volumes of multi-dimensional bioimaging data are now being generated in almost every branch of cell biology and neuroscience, particularly through dynamic imaging and electron microscopy applications. The interpretation and analysis of these image datasets in a quantitative, objective, automatic and efficient manor is a major challenge in current computational biology. The field of bioimage informatics also encompasses both hypothesis- and data-driven exploratory approaches, with an emphasis on how to generate biological knowledge and insights.

BioImage Informatics is an annual meeting in the processing, analysis, and extraction of information and knowledge from biomedical images. The meeting was established in 2005 and has met annually with key leaders in the field and an annual attendance of approximately 200 computational scientists. Previous meetings have been held in Banff 2017, Singapore 2016, NIST USA, 2015, Leuven Belgium, 2014, and Dresden, Germany 2012. The meeting has been influential in the field and is attended by strong researchers and students interested in this informatics domain. With the advent of machine learning applications in cellular resolution science, the significance of these tools and techniques is of increasing value.

BioImage Informatics 2019 meeting themes included:

  • Applications of machine and deep learning to analysis of cellular structure and related function
  • Reconstruction and analysis of neuronal structure and networks
  • Morphological image analysis and its contribution to cell type and cell state and creation of atlases
  • Quantification of dynamic images and transport phenomena
  • Automation of data acquisition and analysis
  • Dynamic cell imaging and biological processes

2019 BioImage Informatics

Registration Cost:

  • Workshop Registration: $50
  • Symposium Registration: $150
  • Student Registration: $150
  • Hackathon Registration: $100

Please contact with any questions.


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Full Program


Event Overview

Monday, October 17:

  • Registration, 12:30-1:00pm
  • Welcome and introduction, 1:00-1:30pm
  • Workshop sessions, 1:30-5:00pm

Tuesday, October 18:

  • Registration, 8:30-9:00am
  • Morning sessions, 9:00-12:00pm
  • Afternoon sessions, 1:00-5:00pm
  • Reception and poster sessions, 5:00-6:00pm

Wednesday, October 19:

  • Registration, 8:30-9:00am
  • Introduction to hackathon challenge, 9:00am-5:00pm

Thursday, October 20:

  • Registration, 8:30-9:00am
  • Hackathon session continued, 9:30am-1:00pm
  • Team presentations and winner annouced, 1:00-2:00pm

Keynote Speakers

  • Anne E. Carpenter, Ph.D., Broad Institute of MIT and Harvard
  • Gaudenz Danuser, Ph.D., UT Southwestern Medical Center
  • Susanne Rafelski, Ph.D., Allen Institute for Cell Science
  • Emma Lundberg, Ph.D., KTH Royal Institute of Technology
  • R. Clay Reid, Ph.D., Allen Institute for Brain Science

CytoData 2022 Local Planning Committee

  • Co-chair: Mike Hawrylycz, Ph.D.,
    Allen Institute for Brain Science
  • Co-chair: Winfried Wiegraebe, Ph.D., Allen Institute for Cell Science
  • Forrest Collman, Ph.D.,
    Allen Institute for Brain Science
  • Gregory Johnson, Ph.D.,
    Allen Institute for Cell Science
  • Lydia Ng, Ph.D.,
    Allen Institute for Brain Science
  • Kaitlyn Casimo, Ph.D.,
    Allen Institute

CytoData Steering Committee

  • Manfred Auer, Ph.D., Lawrence Berkeley National Lab
  • Anne E. Carpenter, Ph.D., Broad Institute of MIT and Harvard
  • Mike Hawrylycz, Ph.D., Allen Institute for Brain Science
  • B. S. Manjunath, Ph.D., University of California, Santa Barbara
  • Gene Myers, Ph.D., Max Planck Institute of Molecular Cell Biology and Genetics
  • Hanchuan Peng, Ph.D. (Chair and Meeting Founder), Allen Institute for Brain Science
  • Jean-Christophe Olivo-Marin, Ph.D., Institut Pasteur
  • Badri Roysam, D.Sc., University of Houston

Pre-Conference Workshop

A pre-conference workshop, "3D Quantitative Visualization of Fluorescently Labeled Cells," will be held on October 1 at the Allen Institute in Seattle, WA. Attendance at the workshop will be by application.

This workshop will cover the 3D visualization, analysis, and presentation of intracellular structures in fluorescence microscope images, and will be taught by members of the Allen Institute for Cell Science team.

Due to the hands-on nature of this workshop and focused, small group discussions, we will limit the number of participants to less than 30. We encourage trainees and bench scientists interested in 3D visual analysis to apply.  We are eager to host a diverse audience at this workshop and will be providing travel awards to a few attendees based on scientific area of interest and financial need.

Applications are due by Friday, July 26, 2019. There is a $50 fee to apply to attend, which will be refunded if your application is not approved for the workshop.

LearN MorE