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.



Phenotyping of tortoise beetles: Automated extraction of morphology from thousands of beetle pictures

Phenotyping of tortoise beetles: Automated extraction of morphology from thousands of beetle pictures...

We want to investigate why populations differ in their ability to evolve and adapt. Our aim is to extract morphological traits, such as body size and shape, from pictures of our study species the green...

Image analysis of bovine embryos

Image analysis of bovine embryos

At SLU in Uppsala, Sweden’s only in vitro embryo production laboratory for agricultural animals is located. The laboratory is well-equipped and has functional embryo production protocols for cattle and pigs. However, just like...

Automated segmentation of testicular biopsies

Automated segmentation of testicular biopsies

Our goal is to utilize artificial intelligence to automate the segmentation of images obtained from patients' testicular biopsies. This approach will enable us to extract large amounts of data and provide both patients and doctors...

Implementing high content screening of chromatin organization in live cells

Implementing high content screening of chromatin organization in live cells

In cells of the human body, inactive heterochromatin tends to distribute in the periphery of the cell nucleus, whereas active euchromatin is mostly localized in the nuclear interior. This spatial organization essential for...

Characterising histological features of salivary glands

Characterising histological features of salivary glands

Our aim in this project was to study salivary glands in the context of gastrointestinal disorders. We are examining H&E-stained sections of mouse salivary glands and characterising known histological features. A necessary task for the...

XRF imaging of an animal model of multiple sclerosis

XRF imaging of an animal model of multiple sclerosis

The idea is to statistically assess elemental distribution and abundance in XRF images measured on spinal cord sections of EAE mice - an animal model of MS. The target is to chemically classify...

Organelle age landscape in skin

Organelle age landscape in skin

Using confocal microscopy and image analysis, we will build a map of the organelle age of different populations in the epidermis.

Droplet microfluidics for detection of bacterial heteroresistance

Droplet microfluidics for detection of bacterial heteroresistance

Antibiotic resistance is a serious medical challenge that puts patients at risk of untreatable bacterial infections and threatens major advances in modern medicine that rely on antibiotics. To tackle this problem, innovative diagnostic...

A spatial single-cell type map of adult human spermatogenesis

A spatial single-cell type map of adult human spermatogenesis

Spermatogenesis involves the transformation of adult spermatogonial stem cells into fully developed sperm cells, which is governed by the testis niche/microenvironment. The cells must maintain a balance between renewing themselves and becoming differentiated, and then...

Evaluation of DNA damage in single cells

Evaluation of DNA damage in single cells

The major aim in this project is to modify an existing comet pipeline developed for Cell Profiler in order to use it for automatic microscopy and image analysis of DNA strand breaks in...

Intracellular location and distribution of proteins with impact of lysosomal movemant and metastasis

Intracellular location and distribution of proteins with impact of lysosomal movemant and metastasis...

The incidence of malignant melanoma has increased during the last decades and UV exposure is the major environmental risk factor. UV irradiation contributes to tumorigenesis by causing direct genetic alterations as well as...

Digitizing historical range maps to estimate range shifts of Nordic vascular plants

Digitizing historical range maps to estimate range shifts of Nordic vascular plants

Quantifying range changes and, importantly, understanding their drivers is vital in a time of ongoing biodiversity change. In this project we use image registration techniques together with GIS analyses to digitize historical range maps of...

Mapping of B cell phenotypes in distinct immune neighborhoods in sarcoma

Mapping of B cell phenotypes in distinct immune neighborhoods in sarcoma

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

DL segmentation for immunofluorescent imaging of mouse brains

DL segmentation for immunofluorescent imaging of mouse brains

In this project, we are looking at immunofluorescent staining of mouse brain cryosections for the study of cerebral cavernous malformations. A necessary task for analysing each image is marking the cerebellum, in effect...

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...

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...

Senolytic compound discovery

Senolytic compound discovery

The aim of the assay is to screen for senolytic compounds capable of clearing senescence cells. For this purpose, we proposed to use an in vitro co-culture of quiescent cells (labeled with a...

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.