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.

For more information, you can contact us at mailto:biif@scilifelab.se.

You can find beyond a collection of ongoing and completed projects supported by the BioImage Informatics Facility.



Mapping of B cell phenotypes in distinct immune neighborhoods in sarcoma

Mapping of B cell phenotypes in distinct immune neighborhoods in sarcoma

Project Description Immunotherapy has lately gained increased attention in sarcoma, but response rates are highly diverse. Therefore, it is essential to identify patient selection criteria and define whether the tumor microenvironment contains responsive immune cells....

Development and characterization of stem cell derived human jejunal organoid models in different formats

Development and characterization of stem cell derived human jejunal organoid models in different...

Our aim is to investigate 3D intestinal enteroids as an in vitro model that more closely reflect the human intestine in vivo as compared to currently used intestinal cancer cell lines

TGFβ family imaging - Simultaneous quantification of RNA levels (RNAscope) and protein levels (IF) in cancer tissue

TGFβ family imaging - Simultaneous quantification of RNA levels (RNAscope) and protein levels...

Project Description Transcriptomic analysis of normal human and cancer cells revealed that the transforming growth factor β (TGFβ) signaling pathway regulates the expression of about 2,000 genes, including protein-coding and non-coding RNAs. Our group uses...

Interactive DL segmentation for neuroimaging data

Interactive DL segmentation for neuroimaging data

In this project, we are looking at combining deep learning (DL) segmentation models with interactive refinement to improve the segmentation of structures like glioblastoma and anerysms in MRI neuroimage data.

CT-Tör 2: Detection of fungus damage in wood

CT-Tör 2: Detection of fungus damage in wood

Törskate is a rust fungus that infects pine trees, primarily in northern Sweden. In this project, the goal is to automatize the detection method in images from laboratory-environment CT-scanners.

In Situ Sequencing of entorhinal cortex in Alzheimer’s disease

In Situ Sequencing of entorhinal cortex in Alzheimer’s disease

The entorhinal cortex is especially relevant for Alzheimer’s disease (AD) pathology. AD initiates in this region at the earliest disease stages, even before the first clinical symptoms appear. Within the entorhinal cortex, layer II excitatory...

Automated detection of vesicles and exocytosis

Automated detection of vesicles and exocytosis

The goal of this project is to quantify protein binding to diffraction limited cellular organelles, for example during the assembly of the machinery for exo- or endocytosis.

TissUUmaps analysis of ISS data in mouse lung tumors

TissUUmaps analysis of ISS data in mouse lung tumors

The goal of the project is to get insight into the communication between tumor cells and immune cells as well as other cells in the tumor microenvironment, and how this is affected by activation or...

LOTUS - Liver Immunology Tissue-resident cells

LOTUS - Liver Immunology Tissue-resident cells

The aim of this project is to functionally evaluate factors involved in tissue-residency of primary human NK cells

Compressed erythrocytes in Cerebral Cavernous Malformations (CCM)

Compressed erythrocytes in Cerebral Cavernous Malformations (CCM)

We study the mechanisms through which CCM originates and progresses using mice models and patient material, amongst other in vitro tools

Mapping Cancer Cell Infiltration and Migration in an Organoid Model

Mapping Cancer Cell Infiltration and Migration in an Organoid Model

The objective of this study is to create a human cancer proliferation and progression model for glioblastoma. To create the model, cerebral organoids cultivated from human induced pluripotent stem cells were cocultured with fluorescent reporter...

Microgel microfluidic platform

Microgel microfluidic platform

We are within this project developing an in vitro method for interaction studies between the constituents of the subcutaneous tissue and different pharmaceuticals.

Chromosome dynamics in live yeast cells

Chromosome dynamics in live yeast cells

The goal of this project is study chromosome organization in live cells and to understand how the spatial organization is affected by inactivation of SMC complexes.

Detecting multiple protein interactions in cancerous tissue using in situ PLA

Detecting multiple protein interactions in cancerous tissue using in situ PLA

In this project, we set out to establish a method to detect multiple protein interactions and protein activation states in different types of cancerous tissue. Building on our long tradition of molecular tools development, we...

Visualization of the Human Development Cell Atlas datasets

Visualization of the Human Development Cell Atlas datasets

The project aim is to create a comprehensive molecular atlas of human prenatal development, describing every cell type in detail and showing their spatial and temporal distributions in three dimensions.

Signaling activation patterns in NSCLC detected by in situ PLA

Signaling activation patterns in NSCLC detected by in situ PLA

Lung cancer is the most common cause of cancer mortality in Sweden and the overall prognosis is poor, with non-small cell lung cancer (NSCLC) representing 85% of all cases. Meanwhile, the underlying processes leading to...

Role of endogenous GDNF in ALS mouse model

Role of endogenous GDNF in ALS mouse model

We hypothesize that increased expression of endogenous GDNF from its native locus may alleviate ALS symptoms

Redox homeostasis regulation induces cardiomyocytes atrophy or hypertrophy

Redox homeostasis regulation induces cardiomyocytes atrophy or hypertrophy

We aim to measure cell geometry alterations by florescence microscopy and to correlate that to molecular data obtained from the same treated cells.

NPC-incorporated structured hydrogels to aid neural cell therapy

NPC-incorporated structured hydrogels to aid neural cell therapy

Aim: To gain knowledge concerning hydrogel potential in neural progenitor cell (NPC) therapy.

In situ Sequencing for Visualization of Tumour Clonal Evolution

In situ Sequencing for Visualization of Tumour Clonal Evolution

Clonal evolution, whereby a single cell in the tumor randomly acquires a mutation conferring a survival benefit followed by expansion of the offspring of this cell in the tumor as a consequence of selection, is...

Ecotoxicology-on-a-chip

Ecotoxicology-on-a-chip

Quantification of the effects of multiple physico-chemical stressors on the metabolism of single cells.

Immunoprofiling of different subtypes of lymphoma using multiplex immunofluorescence

Immunoprofiling of different subtypes of lymphoma using multiplex immunofluorescence

Competition with unshod horses is an important and hot topic in harness racing in Sweden. The performance, when racing unshod, improve markedly compared to the shod condition but trainers and owners are also aware of...

Primary cilia in nervous system development

Primary cilia in nervous system development

Segmentation of primary cilia in nervous system development