BioImage Informatics

The BioImage Informatics Unit 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.

BIIF is a unit of the National Bioinformatics Infrastructure Sweden NBIS, with funding from SciLifeLab, National Microscopy Infrastructure NMI (VR-RFI 2019-00217), and the Chan-Zuckerberg Initiative. We are active within the NEUBIAS and EuroBioImaging networks.

mailto:biif@scilifelab.se(opens in a new tab)

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.
• Dissemination of bioimage analysis knowledge in courses and workshops.
• The AIDA data hub offers Data Sharing, Policy Support, and Services for researchers in Swedish medical imaging AI, and operate the currently largest national AI research system for sensitive personal data in Sweden.

Here is a collection of ongoing and completed projects supported by the BioImage Informatics Unit.

We regularly send out a newsletter informing about upcoming events, workshops, and other relevant information. You can also follow us on Twitter @biif_sweden .

Follow @biif_sweden

CALL4HELP

You can always contact us via biif@scilifelab.se for support on image analysis. Additionally, we offer Call4Help sessions. Here we team up with Sylvie LeGuyader, LCI, Karolinska Institutet. 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.

If you have questions about how to e.g. statistically treat your data after extracting them from images then you might want to join a NBIS drop-in session.

You can find the details about upcoming Call4Help sessions here.

NEWSLETTER

In our newsletter we inform about upcoming courses on bioimage analysis, services of BIIF, and other useful information about bioimage analysis. Just fill-out this google form if you want to be added to our mailing list. You can also read the newsletter online.

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:

Spatial Omics Data Analysis

BIIF within NBIS (National Bioinformatics Infrastructure Sweden) and with the Human Developmental Cell Atlas is organizing a workshop on Spatial Omics Data Analysis. The workshop provides resources to advanced tools for analysis of spatial datasets via a series of online lectures and computer practicals.

More information and application here.

Dates: August 29 – September 3, 2022

Courses and Seminars we teach in on a regular basis:

Digital image analysis for scientific applications – focus MAX IV

The course aims at giving doctoral students and researchers from different disciplines a sufficient understanding of digital image processing and analysis techniques to solve basic image analysis problems. The content of the course includes methods especially suitable for MAX IV data. The course offers an introduction to several freely available software tools (e.g. CellProfiler, ImageJ, and ilastik), preparing the participants to start using computerized image analysis in their research.

More information (past event): https://www.cb.uu.se/~damian/DIASA_2022/

NBIS workshop in Neural Nets and Deep Learning

This course gives an introduction to the concept of Neural Networks (NN) and Deep Learning. Topics covered include:

• NN building blocks, including concepts such as neurons, activation functions, loss functions, gradient descent and back-propagation
• Convolutional Neural Networks
• Recursive Neural Networks
• Autoencoders
• Best practices when designing NNs

More information (past event): https://www.scilifelab.se/event/nbis-workshop-in-neural-nets-and-deep-learning/

LCI microscopy course – From sample preparation to image analysis.

This course provides you with enough theoretical and practical knowledge so that you are able to fully understand how to properly use the hardware and software on your own microscope. It also teaches the principles of image anlaysis. A dedicated workshop on participants’ data gives an understanding on which questions can be addressed using image analysis. More Information: LCI course

BIIF YouTube channel

On the BIIF YouTube channel we upload tutorials on bioimage analysis tools: link

NEUBIAS ACADEMY WEBINARS

We are involved in the organization of NEUBIAS Academy, please find a number of tutorials on image analysis tools here:  http://neubiasacademy.org. Events are recorded and made available online on the NEUBIAS Youtube channel. There you will also our ImageJ/Fiji Macro Scripting link.