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
Project Description 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...
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
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...
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
Project Description 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...
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
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
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
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
Project Description 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
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
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
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)
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
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
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
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
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
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
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...