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From Images to Knowledge with ImageJ & Friends

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From Images to Knowledge with ImageJ & Friends

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November 30 - December 2, 2020
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Discovery in the life-sciences increasingly relies on quantitative analysis of microscopy images. The 2020 virtual workshop “From Images to Knowledge (I2K)”, to be held from November 30 to December 2, will therefore focus on in-depth interactive tutorials covering state-of-the-art open source solutions for biological image reconstruction and analysis, as well as social interaction between developers, researchers, and students. It will be a forum to learn about and discuss forward looking strategies for dealing with the ever increasing amount of large and content rich microscopy imagery.

As all major open source platforms for bioimage analysis will be represented, this will be a great opportunity to learn how to use the best software tools for your research and how to get involved in their development! We will have an exciting number of leaders and rising stars in the field of computational image analysis participating in the workshop, both as tutors and social participants. I2K will therefore be a unique chance to get in touch with them in person.

Topics will include:

  • Bioimage analysis workflows
  • Computer vision and machine learning
  • Handling of big image data
  • Image data annotation and sharing
  • Image data visualisation
  • Image restoration, registration, segmentation, and tracking
  • Smart microscopy
  • Open software engineering

I2K is for (i) researchers and students who are generating or analysing large and/ or complex image data, (ii) scientists creating tools and methods to solve image analysis problems, and (iii) software engineers who provide and maintain the necessary infrastructure.

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Call for Tutorials (deadline October 25, 2020)

Have you created an exciting open-source software tool that solves difficult image analysis problems? Do you develop an open-source library that enables new kinds of visualization or large scale data processing? Are you the creator or expert user of a new machine learning method that can be useful to solve difficult analysis problems? Do you host a database to share large annotated datasets with the scientific community? Anything else that we haven’t thought about? Please apply to host an in-depth tutorial about your work at the virtual I2K 2020 workshop!



We will use Zoom hosted by HHMI Janelia to hold the tutorials. This enables video+audio communication, screen-sharing, and chats. Each tutorial will last up to 4h and will be held twice, once in the morning hours of the tutor’s work-day and once in evening hours of the tutor’s work-day. This guarantees that participants around the planet have access to each tutorial at a reasonable time during their day.

Each tutorial will host a small to medium size group of students. We expect the group size to be between 10 and 20 participants. Tutors will be given the opportunity to decide on the appropriate group size. This small group size enables all participants to interact with each other and with the tutor in real time. Since each tutorial is held twice, it will be available for 2× #participating students. All tutorials will be recorded and will be made available to the public via YouTube or another free video streaming service. Several tutorials will be held concurrently.

Attendees will apply to participate in tutorials at a given time-slot providing a small paragraph describing their background and motivation to join the tutorial. Tutors, together with workshop organizers, will select and assign students to tutorials optimizing for preference and availability.

While the structure of tutorials is the responsibility of the tutor, the following structure may serve as a general guide:

  1. Introduction of the topic, presented by the tutor (20min)
  2. Introduction of each student and their background, presented by the students (2-5min each, 50min)
  3. Practical work and training (2.5h)
  4. Summary and questions (1h)

Please send a proposal to the workshop organizers. Your proposal must include:

  • Information about the tutor[s].
  • Title and abstract of the tutorial.
  • A rough outline how the tutorial will be organized including technical requirements.
  • At what time of the day you will be able to host the tutorials.

Workshop organizers will help tutors to make sure that technical requirements can be met. One workshop organizer/ assistant will be available during each tutorial to help with technical and administrative issues (including recording). Tutorials will be distributed over the three days from Monday, November 30 through Wednesday, December 2, 2020 at the time of day that the tutor proposed.

Meet your peers

Social interaction will be facilitated by virtual receptions during which school participants are encouraged to be available for small group meetings with Zoom (virtual tables). All attendees are registered with a dedicated Zoom channel such that they can see other attendees and their availability for video, audio, or text chat. During a virtual reception, we will display a list of virtual tables and their attendees such that other attendees can join existing virtual tables or create new virtual tables as necessary. The size of each virtual table will be limited to 5 attendees such that meetings are truly interactive. Senior attendees (PIs, tutors, organizers) will be encouraged to make themselves available to younger attendees by joining existing virtual tables or creating their own. We also envision that tables will be used for paired or group programming sessions, so that people who usually do not work together are enabled to do so on a specific problem, framework, or language.


Stephan Preibisch, Janelia Research Campus/HHMI
Stephan Saalfeld, Janelia Research Campus/HHMI
Anna Kreshuk, European Molecular Biology Laboratory
Pavel Tomancak, Max Planck Institute of Molecular Cell Biology and Genetics
Virginie Uhlmann, European Molecular Biology Laboratory