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Bioimage Informatics Call4Help

Every 1st week of the month (mainly on Tuesdays, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate.

The ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji, CellProfiler, KNIME, QuPath, Ilastik), but also commercial systems, if needed (Imaris).

How to participate?


Prepare a short presentation (5-7 min)  – use the following template for your presentation:


a) Upload your presentation to the following google drive or to a different link.

b) Upload example images for testing. Either to the google drive above or to a different link.

c) Register by filling out the registration form:

Step 3:

Join the zoom-session (the link will be sent to the participants beforehand). The session will start at 9.00 and end at the latest at 12.00, depending on the number of presentations.

If your problem is selected for presentation, you will get a time-slot of 30 minutes within the session. If not, you are welcome to join the discussion anyway!

What are the Deadlines

Submission of a problem and upload of example data: Friday the week before the session.

Notification about participation: The day before the session.

Next Call4Help session

Tuesday, October 6, 2020, 9.00-12.00. Deadline for application: Friday, October 2, 2020.