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.

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



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

Horse hoof analysis

Horse hoof analysis

This project aims for investigating potential morphological differences between horse that are able to compete unshod and horses that need to have shoes during races.

Automatic motion artifact detection for in vivo confocal image stacks

Automatic motion artifact detection for in vivo confocal image stacks

Acquisition of 4D in vivo confocal data from anesthetized mice is a complex task that involves overcoming a myriad of challenges such as proper surgical preparation, monitoring of vital physiological parameters of the anesthetized animal...

Cancer-induced vascular changes

Cancer-induced vascular changes

Lymph node tumor metastasis is one of the most important prognostic factors in human cancer and correlate with an increased risk for further metastatic spread in several types of cancer, including breast cancer and pancreatic...

Quantification of vessel and vessel lumen area in tissue sections

Quantification of vessel and vessel lumen area in tissue sections

In a list of fluorescent images of mouse lymph nodes, we want to measure the total area of the lymph nodes, the total area of lymphatic vessels and the total area of the lumen within...

Piezo1 activation attenuates thrombin-induced blebbing in breast cancer cells

Piezo1 activation attenuates thrombin-induced blebbing in breast cancer cells

Amoeboid cell migration, facilitated by the formation of dynamic plasma membrane blebs, is implicated in cancer cell migration, particularly in compressive environments such as those found in growing tumors. Blebbing is initiated by localized dissociations...

Ratio calculation for auxin quantification in Populus R2D2 roots

Ratio calculation for auxin quantification in Populus R2D2 roots

Project Description Root growth in plants is regulated by the phytohormone auxin. Auxin forms a gradient in root tissues with a concentration maximum at the root tip. The gradient conveys positional information that regulate cell...