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BioImage Informatics

National facility

The BioImage Informatics Facility provides support and education in image analysis. We develop computational methods that automatically analyze and understand images of biological processes, using microscopic images as their primary source of information. We draw upon methods from computer vision, machine learning, statistics, and bioinformatics to quantify image data and answer biological questions. We do not primarily analyze data for our users, but rather help users get started with their own analysis. The SciLifeLab BioImage Informatics Facility has two nodes; one in Stockholm, connected to the School of Computer Science and Communication at KTH, and one in Uppsala, at the Centre for Image Analysis, Dept. of Information Technology, Uppsala University.

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

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:

CALL4HELP

Every 1st Tuesday of the month 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?

Step1:

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

https://docs.google.com/presentation/d/19dsu95_6MyzQtyBz-hvf_bOgHj_rs9f4_6tEMQITCc4/edit?usp=sharing

Step2:

a) Upload your presentation to the following google drive

https://drive.google.com/drive/folders/1jDsMtoW3_yaE_vyr6CkC9tKpn5X6fHR8?usp=sharing 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: https://docs.google.com/forms/d/e/1FAIpQLSe9HqrfVC7n279RvTgbXa9RmQIlwsMwwuS9KBxOgyj_Ujg3eg/viewform?usp=pp_url

Step 3:

We will send around a zoom-link before the session. Join by following the link.

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: one week before the session (Tuesday)

Notification about participation: Thursday of the week before the session

Session: 1st Tuesday/month 9:00-12:00. If this is a holiday we will announce a different day. There will be no sessions in July and August.

RECENT PROJECTS

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