• Are you facing a problem in bioimage analysis?

    Have you’ve already spend hours/days on problem-solving and your results are, at best, unimpressive?

    You've come to the right place!

     

    Call 4 Help: BioImage Analysis

  • What is Call4Help?

    It's a go-to place for when you need help with your Image Data

    Originally a panel-discussion during the NEUBIAS2020 conference in Lisbon 2017, Call4Help has since evolved to its current form:

    A website bringing together members of the (Bio-)Image Data Scientist community and life-sciences to present their problems and share their suggested solutions.

     

    Here you can present your case, see other presentations and share your thoughts and hints. You can also find information about upcoming Call4Help events and how to take part in them.

  • It's simple

    Create a presentation, share it with the community and get hints on possible solutions

    Step 1

    Create a presentation using our template in Google Slides

    Step 2

    Fill the submission form and share your presentation

    Step 3

    Get the help you need - during a session or later via #call4help on ImageJ forum

  • Cases

    Watch presentations and share your insights

    Annotation tools for cells in 3D microscopy images

    Alvaro Gomariz (ETH Zurich)

    Published: 2018-04-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    About Alvaro: [link]

    Qualitative characterization of skeletal muscle mitochondria dynamics to relate them to OXPHOS

    Clara Prats (University of Copenhagen)

    Published: 2018-04-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    About Clara: [link]

    Automated synaptic spot selection for time series analysis

    Katharina Schneider (German Center for Neurodegenerative Diseases [DZNE e.V.], Garner lab, CharitéCrossOver)

    Published: 2018-04-19

     

    Presentation [link]

    Raw Data [link]

    Discussion [link]

    About Katharina: [link]

    Multiplexed imaging of kinases activity upon G-protein activation

    Sergei Chavez Abiega (University of Amsterdam)

    Published: 2018-04-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    About Sergei: [-]

    Synchrotron Radiation-Based X-Ray Phase Contrast Imaging of Human Myocardium

    Patricia Garcia-Canadilla (Universitat Pompeu Fabra)

    Published: 2018-04-19

     

    Presentation [link]

    Raw Data [link]

    Discussion [link]

    About Patricia: [link]

    Extracting “fiber like” structures from a “not so good” image

    Bertrand Cinquin (CNRS, LBPA ENS Cachan)

    Published: 2018-04-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    About Bertrand: [-]

    Recognition of mast cells in tissues histology sections

    Fabrizio Radaelli (Università degli Studi di Milano-Bicocca)

    Published: 2018-04-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    About Fabrizio: [-]

    The eyes are the windows to the soul (i.e. general chromatin state)

    Joyce Kao (NYU/ETHZ)

    Published: 2018-04-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    About Joyce: [link]

    The eyes are the windows to the soul (i.e. general chromatin state)

    Endre Kókai (University of Debrecen)

    Published: 2018-04-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    About Endre: [-]

    Automatic quantification of filaments

    Christina Braunsdorf

    (LeibundGut Lab,Group of Immunology,University of Zürich)

     

    Published: 2017-11-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    About Christina: [link]

    High Content Imaging screening in primary neurons

    Elisa Nerli (University of Trieste)

    Published: 2017-11-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    About Elisa: [link]

    Measuring mitochondria from TEM images of BAT

    Igor Golic (University of Belgrade)

    Published: 2017-11-19

     

    Presentation [link]

    Raw Data [-]

    Discussion [link]

    Intravital imaging and 4D quantification of tumor growth and the tumor vasculature

    Marta Alabrudzinska (Karolinska Institutet)

    Published: 2017-03-14

     

    Presentation [link]

    Raw Data [-]

    LiveNotes [link]

    Discussion [link]

    About Marta [link]

    Quantifying Myelin Profile Thickness from TEM images of CNS cross-sections

    Team: Ofra Golani, Anya Vainshtein, Christina Katanov, Elior Peles (Weizmann Institute of Science)

    Published: 2017-03-14

     

    Presentation [link]

    Raw Data [-]

    LiveNotes [link]

    Discussion [link]

    About Ofra [link]

    Quantifcation of myelinated Axons in the corpus callosum

    Thomas Lendl (IMP Vienna)

    Published: 2017-03-14

     

    Presentation [link]

    Raw Data [-]

    LiveNotes [link]

    Discussion [link]

    About Thomas [link]

     

    Intravital imaging and 4D quantification of tumor growth and the tumor vasculature

    Peter Zentis (CECAD – University of Cologne)

    Published: 2017-03-14

     

    Presentation [link]

    Raw Data [-]

    LiveNotes [link]

    Discussion [link]

    About Peter [link]

    Does Upregulation of Transcription Factor Determine Cell Survival?

    Heiko Dussmann (Royal College of Surgeons in Ireland)

    Published: 2017-03-14

     

    Presentation [link]

    Raw Data [-]

    LiveNotes [link]

    Discussion [link]

    About Heiko [link]

    Additional materials [link]

    Volume Electron Microscopy Image Analysis

    Martin Jones (Electron Microscopy Science Technology Platform, The Francis Crick Institute)

    Published: 2017-03-14

     

    Presentation [link]

    Raw Data [-]

    LiveNotes [link]

    Discussion [link]

    About Martin [link]

    Quantification of cardiac micro-structures on intact whole heart using synchrotron X-ray imaging​

    Team: Chong Zhang, Patricia Garcia-Canadilla, Hector Dejea, Anne Bonnin, Vedrana Balicevic, Marco Stampanoni, Bart Bijnens, Andrew C. Cook

    Published: 2017-03-14

     

    Presentation [link]

    Raw Data [-]

    LiveNotes [link]

    Discussion [link]

    About Chong [link]

  • Guidelines

    To ensure all relevant information is available, please ensure that...

    • Your presentation takes no more than 3 minutes to present

    • You use our presentation template (we ask that you use Google Slides to facilitate sharing and commenting)

    • Your presentation includes

      • An introduction of the project's context to a broader audience

      • Example images (adapted for projector viewing -- big fonts, minimal text)

      • List of desired outputs and challenges in order of importance

      • (optional) Overview of what you have tried so far and where it worked/failed

    • You submit your presentation using our submission form 

    If you wish to present your case during the next Call4Help event

      • Let us know by marking it on your submission form
      • Be brief and keep it simple: If you have many questions, please split them into multiple presentations
      • Ensure that the images in your presentation are adjusted for maximum clarity of your message  (enhance contrast, use colormaps, etc.)

      Call4Help sessions during events - how does it work?

      • We simply run your problems one by one. Each case gets about 10 minutes - 3' for presentation, and 7' for discussion
      • Usually, the audience is very diverse - from life scientists via tool developers to computer vision experts - it gives you an opportunity to pick the brains of experts from many fields, simultaneously
      • During a session we make notes using Google Docs. You can find them on this site and add your thoughts also later

      Q&A

      • Q: I would like to include videos in the presentation. Is it possible?
        • A: Yes, however, to include a video in Google Presentation a video needs to be uploaded. Please use: Insert > Video and follow the on-screen instructions.
    • Submission Form

      Please submit your problem here

    • Resources

      Quick links

      See what your presentation should look like

      Use it to create your own presentation

      Use it to submit your work

      LiveNotes from NEUBIAS2020

      Check the output of our first event

    • Events

      Events where Call4Help session are organized

      2nd NEUBIAS Conference

      31st Jan. - 2nd Feb. 2018, Hungary

      The 2nd Annual Conference of NEUBIAS, gathering the whole BioImage Analysis Community into a multi-faceted event, offers two Training schools, a Working Meeting (Taggathon) and a Large Symposium dedicated to Scientific Developments and Open Tools in BioImage Analysis. [more about the conference]

      Past events

      ZIDAS 2017

      16th - 20th October 2017, Switzerland

      This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples. You will learn the fundamentals of image analysis, including basic macro programming in ImageJ/Fiji as well as other software solutions. In the first part of the week we will also cover the process of image-formationas it pertains to image analysis: Resolution, correct exposure, point-spread functions, detector noise, Shannon's sampling theorem, and aliasing. All with a clear focus on application in the lab. [more about the conference]

      BIAS

      14-20 May 2017, Germany

      Organised by EMBL, the topics of this conference reflect the scientific research carried out by EMBL scientists or bring together long established communities sometimes outside the realm of EMBL research. This platform allows for the exchange of our exciting findings with the international scientific community.

      [more about the conference]

      NEUBIAS2020

      12-17 Feb. 2017, Portugal

      NEUBIAS2020 conferences bring together Life-Scientists, Bioimage Analysts, Image Analysis- and Software- developers and other Core Facilities Specialists (e.g. Microscopists) to bridge the gap between Bioimage Analysis developments and know-how, and their use in Life Science. It aims to be a forum to exchange the newest findings, applications and cutting-edge developments in Bioimage Analysis, machine learning, data mining and storage.

      [more about the conference]

    • Contact Us

      Don't be afraid to reach out

      ETH Zurich
      Scientific Center for Optical and Electron Microscopy
      ScopeM (HPI F15/F17)
      Wolfgang-Pauli-Str 14
      8093 Zurich