BioImage Informatics

Infrastructure Unit

Contact

biif@scilifelab.se

Anna Klemm, Head of Unit

anna.klemm@it.uu.se+46 72 – 701 06 57

Carolina Wählby Platform Scientific Director

carolina.wahlby@it.uu.se+46 18 4713473


Recent user publications

The publications in this database are the result of research conducted at the units of SciLifeLab – both in user projects and technology development.

Personnel

Anna Klemm
Head of Unit
+46 (0)72 – 701 06 57

Carolina Wählby 
Platform Scientific Director
+46 (0)18-471 34 73

Christophe Avenel
Bioimage Analyst

Fredrik Nysjö
Bioimage Analyst

Jonas Windhager
Bioimage Analyst

Kevin Smith
Unit Co-director, Stockholm
+46 (0)8-790 64 37

Gisele Miranda 
Bioimage Analyst

Affiliated with BIIF:

Amin Allalou 
Researcher, danioreadout Zebrafish facility, Uppsala

Ida-Maria Sintorn 
Professor Image Processing, Dept. Information Technology Uppsala
focus on electron microscopy and automated microscopy

 

 

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 – see examples on our project database. 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, write us an email, or fill-out the NBIS support form. 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.

project website: biifsweden.github.io
biif@scilifelab.se

OPEN POSITION

We are looking for a Bioinformatician with focus on image analysis and supporting researchers all over Sweden. Read more about the position and apply here.

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 .

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.

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 events:

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. Lectures are broadcasted live on Zoom! More Information: LCI course

Effectively Communicating Bioimage Analysis

Bioimage analysis is a critically needed discipline, especially as the number of new tools is exploding as part of the “deep learning revolution” and as larger data sizes and automated screening systems make manual data handling of microscopy data increasingly impractical. While there are more educational and training materials than ever, a few major challenges still exist.
In this Workshop, we aim to:

  • Map our “landscape”
  • Bring together both users and creators of training materials and courses
  • Curate the resources that currently exist, and brainstorm how these can be shared more effectively or used in novel ways
  • Create a draft set of standards to recommend to stakeholders

More information here.
Dates: February 12-15, 2024, Buxted Park, East Sussex, UK 

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 here.

Courses and Seminars we are involved in:

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 exercises. More information here.

EMBO Practical Course: Advanced methods in bioimage analysis

This advanced course concentrates on teaching cutting-edge concepts and tools for quantitative image analysis and seeks to upgrade the competencies of future bioimage analysis experts on both theoretical algorithm advancements as well as on practical implementation skills.

  • Microscopy image quality control and image restoration
  • Advanced image segmentation and complex cell phenotyping
  • Handling large microscopy images (such as whole slide scans) and big N-dimensional data 
  • Neural-networks for image restoration, segmentation, and object classification.
  • Co-localisation and spatial statistics
  • Train the trainer: how to teach image analysis

More information here.


Digital image analysis for scientific applications

This course aims at giving doctoral students and researchers from different disciplines sufficient understanding to solve basic computerized image analysis problems. The course offers an introduction to a number of freely available software tools, preparing the participants to start using computerized image analysis in their own research.

More information available here.

Introduction in Image analysis for Life science, Graduate course, CCI, Göteborg

The focus of the course is on reaching a broad understanding of computerized image analysis in Life Science (mainly fluorescence and electron microscopy images) and a basic understanding of the theory and algorithms behind the image analysis methods and tools. Hands-on exercises that will teach a broad functionality of these tools and the concepts needed for building suitable workflow for a given application. More information on the CCI course website.

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.

NBIS Long-term Support

The NBIS Bioinformatics Long-term Support offers extensive bioinformatics support to a limited set of scientifically outstanding projects. This support has been enabled primarily by a generous grant from Knut and Alice Wallenberg Foundation (KAW). The idea is simple: A senior bioinformatician will work in your project 500 hours for free. Hands-on involvement by the applying research group is strictly required to ensure efficient knowledge transfer.

More information here .

Uppsala

Mail address

Vi3, Department of Information Technology
Lägerhyddsv. 1,
751 05 Uppsala

Visitor address / Deliveries

Vi3, Department of Information Technology
Lägerhyddsv. 1,
751 05 Uppsala

Stockholm

Mail address

Scilifelab
Bioimage informatics
Box 1031
171 21 Solna

Visitor address / Deliveries

Scilifelab
Bioimage informatics
Tomtebodav 23A
171 65 Solna

Last updated: 2024-02-07

Content Responsible: admin(website@scilifelab.se)