Gastrointestinal tissue-samples from population-based endoscopy studies
The project consists of gastrointestinal tissue-samples from 3 population-based endoscopy studies. In all three studies a random selection from the general population was included. In the Kalixanda upper endoscopy study includes biopsies from 1000 individuals,...
The role of perivascular TAM phenotypes in metastatic dissemination
Accumulation of Tumor-Associated Macrophages (TAMs) is associated with enhanced tumor progression and poor survival in most solid cancers. TAMs are plastic cells exhibiting states and phenotypes spanning from anti-tumor/immunostimulating (sometimes referred to as...
Optimization of Particle Tracking in Mucus
Nanoparticles as carriers of drug would diffuse in different speed depending on the interaction with the medium. In the colonic environment, one of the barriers would be the colonic mucus and we are...
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...
Pathological characterization of cardiac tissue samples from dogs in various stages of myxomatous...
Histopathology will be employed to characterize cardiac tissue samples collected from dogs affected by Myxomatous Mitral Valve Disease (MMVD) or Dilated Cardiomyopathy (DCM) to increase knowledge about the cardiac remodeling process in cardiac diseased dogs....
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
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
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
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
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
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
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
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
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...
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
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
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
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...
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.