BioImage Informatics Facility Projects

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.



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...

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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...

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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...

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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...

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Image analysis of cardiovascular and metabolic risk factors in 10 day-old zebrafish larvae.

Image analysis of cardiovascular and metabolic risk factors in 10 day-old zebrafish larvae....

Project Description The den Hoed research group at IGP has acquired imaging data for traits related to cardiovascular and metabolic diseases in >25,000 larvae since 2014. Image analysis pipelines have previously been developed for these...

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Defining the basal layer in the ectocervical epithelium

Defining the basal layer in the ectocervical epithelium

Design of an image analysis pipeline which allows for automatic detection of the basal membrane/layer.

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Feature extraction from tissue section output images

Feature extraction from tissue section output images

Sectioning of formalin fixed tissues is a convenient way of obtaining image information on cell morphology and how cells make up tissues. The sections are usually stained with hematoxylin and eosin to...

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Fra-1 and PARP-1 in breast cancer

Fra-1 and PARP-1 in breast cancer

Fra-1, a member of the activator protein 1 (AP-1) family, is overexpressed in triple-negative breast cancer (TNBC). Our group has identified in previous research that there are 118 proteins interact with endogenous chromatin-bound Fra-1 in...

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DoUble resin casting microCT (DUCT) reveals biliary and vascular pathology in tandem in a mouse model of Alagille syndrome

DoUble resin casting microCT (DUCT) reveals biliary and vascular pathology in tandem in...

We developed double resin casting micro computed tomography (DUCT) as a new tool to visualize and automatically quantify the architecture of lumenized systems in vivo in tandem. We applied this novel...

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zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging

zOPT: an open source optical projection tomography system and methods for rapid 3D...

We have developed an Optical Projection Tomography platform for 3D imaging of zebrafish. The system is used in several projects in collaboration with Genome Engineering Zebrafish, SciLifeLab.

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Searching for genetic targets for nonalcoholic fatty liver disease (NAFLD) and related diseases

Searching for genetic targets for nonalcoholic fatty liver disease (NAFLD) and related diseases...

Obesity is rising worldwide due to an increase in total energy consumption and changes in life stiles. This pandemic growth has resulted in an increased incidence of obesity-associated nonalcoholic f...

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Effects of repeated intraportal islet transplantation on islet engraftment in a GFP mouse model

Effects of repeated intraportal islet transplantation on islet engraftment in a GFP mouse...

The outcome of islet transplantation has improved progressively. However, the lack of organ donors makes islet transplantation available only to patients with type I diabetes with the most severe gly...

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KNIME support for High-Content Screening

KNIME support for High-Content Screening

KNIME is a free and open-source data analytics platform. It is very suitable to sort, filter, analyze and display data obtained in High Content Screens. In this project data-normalization, filtering a...

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Probing the role of Atox1 in breast cancer cell migration

Probing the role of Atox1 in breast cancer cell migration

We study the role of Atox1 in breast cancer cell migration. Atox1 is a cytoplasmic Cu transporter and is overexpressed in breast cancer tissue. Previously, we observed using wound healing studies tha...

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Biomaterials for bone defects-image analysis of cell cultures

Biomaterials for bone defects-image analysis of cell cultures

Bone defects are a common and sometimes very difficult problem in the patient population. If the body can’t heal the defect by itself, the gold standard treatment is bone grafting. This type of...

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Identifying novel small molecule drugs for CCM treatment

Identifying novel small molecule drugs for CCM treatment

We are identifying modulators of VE-cadherin formation in images generated in a small molecule drug screen. We use CellProfiler to detect and quantify changes, and KNIME for automated classification ...

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Linking cell cycle with protein expression

Linking cell cycle with protein expression

Pilot studies to characterize protein expression changes in human embryonic stem cells during the different cell cycle stages is led by Gallant group. They observed highly differential regulation of c...

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Development of a fat phantom

Development of a fat phantom

Phantoms that closely mimic the dielectric properties of human tissues play an important role in testing and evaluating devices and various treatment and diagnostic schemes. A phantom is a physical m...

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Analysis of fluorescent intensity in brain slices

Analysis of fluorescent intensity in brain slices

We automatically segment brain slices in large tile scans. In the brain area we measure the fluorescent intensity of different markers using automatic thresholding. ...

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Imaging mass spectrometry of mouse implantation sites

Imaging mass spectrometry of mouse implantation sites

Mass spectrometry imaging enables visualization of the chemical microenvironment in regional features within thin tissue sections. In this project, thin tissue sections of mouse embryo implantation s...

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Automated Detection and Counting of Cells in Zebrafish

Automated Detection and Counting of Cells in Zebrafish

Large-scale genome-wide association studies have identified numerous loci that are robustly associated with blood cell count. Identifying and characterizing causal genes in these loci using in vivo mo...

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Vgluts, alcohol and nicotine

Vgluts, alcohol and nicotine

Initiation of alcohol and nicotine use in early age is a well-known risk factor for the development of addiction. The glutamatergic system plays an important role in mediating the reinforcing effects...

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Effects of a mixture of endocrine disrupting compounds on growth and metabolism in a chicken embryo model

Effects of a mixture of endocrine disrupting compounds on growth and metabolism in...

The project is part of an EU project called EDC-MixRisk which aims to improve our understanding of health effects of endocrine disrupting chemicals. In EDC-MixRisk, a mixture of common chemicals have...

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Intracellular trafficking pathways of PDGFRb

Intracellular trafficking pathways of PDGFRb

This project investigates trafficking pathways of PDGFRb from the cell surface upon activation with PDGF-BB ligand. PDGFRb is known to form dot-like clusters upon activation that only partially co-lo...

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Imaging protein synthesis in primary cortical neuronal culture using Click-iT® Plus OPP Protein Synthesis Assay Kits

Imaging protein synthesis in primary cortical neuronal culture using Click-iT® Plus OPP Protein...

The goal of this project is to analyze protein translation rate in mouse primary cortical neurons and astrocytes. The aim is to assess the protein synthesis by using the OPP Kit in primary cortical c......

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Applying semi-automated histology-to-radiology co-registration in en bloc resected gliomas

Applying semi-automated histology-to-radiology co-registration in en bloc resected gliomas

Gliomas are heterogeneous tumors in terms of imaging appearances, and a deeper understanding of the histopathological tumor characteristics that underlie the signal abnormalities on PET and MRI is ne...

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Human induced pluripotent cells derived neuroepithelial-like cells differentiation potential in the presence of the mouse auditory brainstem milieu

Human induced pluripotent cells derived neuroepithelial-like cells differentiation potential in the presence of...

Stem cell therapy has been proposed as an option to treat sensorineural hearing loss since auditory system as well as the most of the central nervous system has a limited regenerative potential. The ...

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Effect of perfluorononanoic acid (PFNA) on early embryo development in vitro

Effect of perfluorononanoic acid (PFNA) on early embryo development in vitro

For the last decades a concern has been raised that female fertility is declining – more than could be explained by the fact that we choose to have children later in life and possible genetic...

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In vivo modeling of high grade glioma for oncology drug developments

In vivo modeling of high grade glioma for oncology drug developments

The main goal of this study was to develop a platform for quantifying the tumor-initiating capacity of a large panel of glioma-stem cell cultures (GSCs) in adult mouse brain to define the cancer ste...

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Automated quantification of axonal growth

Automated quantification of axonal growth

The aim of this project is to establish a standardised method for measuring cell and axonal growth from spinal cord slice cultures. To measure the area of axons outside the explant body, pictures of...

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Effects of mixtures of endocrine disrupting compounds (EDC) on Wnt/beta-catenin signaling in developing zebrafish

Effects of mixtures of endocrine disrupting compounds (EDC) on Wnt/beta-catenin signaling in developing...

Wnt/beta-catenin signaling is involved in proliferation and fate of cells thus playing fundamental roles during embryo development. The specific aims of this part of the EU project are to 1) develo...

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Infiltration of T Cells in Thyroid Glands

Infiltration of T Cells in Thyroid Glands

The aim of the project is to estimate the degree of infiltration of T cells in thyroid glands of chicken in order to better understand auto-immunity and rare genetic disease. We have developed an im......

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Assessing Bacterial Growth Kinetics and Morphology Using Time-lapse Microscopy Data

Assessing Bacterial Growth Kinetics and Morphology Using Time-lapse Microscopy Data

In vitro methods are often used to study the concentration-effect relationship for antimicrobial agents. Time-kill curve experiments have long been the standard methodology, with bacterial counts f...

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Quantification of lipid droplets in human pre-adipocyte

Quantification of lipid droplets in human pre-adipocyte

Adipocytes store lipids, predominantly triglycerides (TGs), in lipid droplets (LDs). Upon energy shortage, TGs are hydrolyzed into non-esterified fatty acids and glycerol in an enzymatic process term...

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Amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis is a neurodegenerative disease characterized by the loss of motor neurons in the cortex brain stem and spinal chord. The incidence is 1 in 50 000 combining US and EU po...

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Kidney Morphology and Topology of the Glomerular Filtration Barrier

Kidney Morphology and Topology of the Glomerular Filtration Barrier

Our collaborators have developed a super-resolution immunofluorescence microscopy protocol for the study of the filtration barrier in the kidney. The aim of the project is to quantitatively evaluate...

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Analysis of Keratin Aggregates

Analysis of Keratin Aggregates

Epidermolytic hyperkeratosis (EH) is a rare genetic skin disorder caused by mutation of keratin 1 or 10, and characterized by blistering in the epidermis and hyperkeratosis. The skin may blister eas...

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Rat Spinal Cord

Rat Spinal Cord

Our collaborators newly established an way of staining the activity in the endogenous opioid system in the rat spinal cord, and the aim of the project is to quantify the ammount and localization of ......

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Cell Distribution and Protein Expression in the Ectocervix

Cell Distribution and Protein Expression in the Ectocervix

The female genital mucosa presents a comprehensive natural immune defense against HIV infection, although during exposure to a high dose of virus this is not enough to protect the individual against...

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Ubiquitin Screen

Ubiquitin Screen

Ubiquitin is a small protein that is found in almost all cellular tissues in humans and other eukaryotic organisms, which helps to regulate the processes of other proteins in the body. Cultured cell...

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Cell Time-Lapse Analysis

Cell Time-Lapse Analysis

he aim of the project is to interpret differences in migration-proliferation of cells with different treatments and express those in a quantitative manner. We used a 'scratch assay' approach, or 'wo...

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Vascular Networks

Vascular Networks

In this project we analyze vascular networks in the mouse brain, retina networks and cell junction activations. We have several applications where we skeletonize the networks and extract branch poin...

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Segmentation of Neurons

Segmentation of Neurons

The goal of this project is to analyze neurons grown from stem cells in vitro. The aim is to assess the percentage of neurons (using B-tubulin) and certain neuron subtypes (GABA) by immunofluorescen...

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Quantification of Zebrafish Lipid Droplets

Quantification of Zebrafish Lipid Droplets

The aim of this project is to identify novel targets for the therapeutic intervention of coronary artery disease. This is done by following-up results from genome-wide association studies in epidemi...

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