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BioImage Analysis support – Call4Help

April 5, 09:00 - 12:00

Organizer

Bioimage Informatics Unit
biif@scilifelab.se
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Venue

Online event via Zoom
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BioImage Analysis support – Call4Help

April 5, 2022 @ 09:00 12:00 CEST

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, QuPath, Ilastik, KNIME), but also commercial systems, if needed (Imaris).

The Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM.

How to participate?

Step1:

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

http://bit.ly/BIIF_C4H_slideTemplate

Slide template by NEUBIAS/ScopeM

Step2:

a) Upload your presentation

Upload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over.

http://bit.ly/BIIF_C4H_Drive

b) Upload example images for testing.

Upload example images for testing either to the drive of your choice or our Call4Help google drive above.

http://bit.ly/BIIF_C4H_Drive

c) Register by filling out the registration form:

http://bit.ly/BIIF_C4H_Registration

Step 3:

Join the zoom-session.

If your problem is selected for presentation, you will get a time-slot of 30 – 60 minutes within the session.

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, April 5, 2022, 9.00-12.00. Deadline for application: Friday, April 1, 2022.