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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.

SERVICES

  •  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

CALL4HELP

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.

 

COURSES AND WORKSHOPS

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:

  • Open-Source Image Analysis Tools, Microscopy Course, Biomedicum Imaging Unit, Helsinki, 11 May 2020
  • Image Analysis Introduction, Bioimaging and Cell Analysis, 3MG036, Uppsala, 8/9/10 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

NEUBIAS ACADEMY WEBINARS

We are involved in the organization of NEUBIAS Academy http://neubiasacademy.org.

Upcoming webinars:

14 May 2020: A survey of contemporary computer vision tasks and advanced Python programming for image processing, Register now

19 May 2020: Tracking cells and organelles with TrackMate, Register now

20 May 2020: Writing or modifying your own CellProfiler modules, Register now

26 May: Introduction to 3D Image Analysis with ImageJ 3D suite, by Thomas Boudier, will soon open for registration.

4 June: Multi-dimensional image visualization in Python using napari, by Nicholas Sofroniew Register Now

FOLLOW UP SESSIONS:

13 May: Interactive Bioimage Analysis with Python and Jupyter, by Guillaume Witz. Watch Part 1 here, Register now

Youtube Videos:

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

ImageJ/Fiji Macro Scripting link

RECENT PROJECTS

Publications where the BioImage Informatics Facility has been involved:
https://publications.scilifelab.se/label/BioImage%20Informatics