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BioImage Informatics

National facility

The BioImage Informatics Facility provides the support and training you need to perform state-of-the-art analyses on your image data. Our experts can help you deploy computational methods using computer vision, machine learning, and bioinformatics to analyze your images. Whether you are looking for training on how to use existing software solutions or help developing a custom workflow, we can help you get your analysis running.

Contact us in person, join a Call4Help, or write us an email. We usually respond fast and are always open to new ideas. You can visit us at one of our two locations: at the SciLifeLab Solna campus, or at the Centre for Image Analysis in Uppsala.


  •  Advice on best-practice and guidance on overall experimental design (staining, sample preparation, and image acquisition) for research involving microscopy imaging and quantitative data analysis.
  • Guidance on image analysis assay development, including image processing algorithm development and software engineering to address challenging project goals.
  • Advice on best-practice and guidance on high throughput/large-scale image processing using computing clusters, including data transfer and storage during the activity of the project.
  • Guidance on large-scale data analysis and visualization


The BioImage Informatics Facility organizes a monthly online help session open to all Swedish researchers together with microscopy expert Sylvie Le Guyader. During the Call4Help session you will have access to expert advice covering all aspects of your image analysis research - from the acquisition of digital images to the finished analysis.

The ideal time to join a Call4Help session is after you have performed some initial pilot experiments but before you have started collecting large amounts of data in earnest.

Next upcoming session is on Tuesday June 2, 9.00-12.00. You can find the details here.



Part of our research support is provided in the form of courses, workshops and invited talks at courses related to digital image processing and analysis in life science.

Upcoming Courses and Seminars where we are involved:

  • Image Analysis Introduction, Bioimaging and Cell Analysis, 3MG036, Uppsala, 8/9/10 September 2020
  • PhD course Cancer Drug Discovery, KI, 10 September 2020
  • Advanced Methods in Bioimage Analysis, EMBL Heidelberg, 03-09 October 2020, link
  • PhD course on DIASA - Digital Image Analysis for Scientific Applications (organized by Ingela Nyström) starting in October 2020


We are involved in the organization of NEUBIAS Academy

Upcoming webinars:

11 June: A guided tour for analyzing and quantifying single-molecule localization microscopy data by Siân Culley & Florian Levet, Register now


Youtube Videos:

Events are recorded and made available online on the NEUBIAS Youtube channel.

ImageJ/Fiji Macro Scripting link


Publications where the BioImage Informatics Facility has been involved: