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
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
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...
Image analysis of cardiovascular and metabolic risk factors in 10 day-old zebrafish larvae....
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...
An image-based analysis of recombinant silk fiber structures
The overall goal is to set up and implement an image-based analysis workflow to identify significant features of recombinant silk fibers as revealed by light microscopy.
Analysis of Bile ducts around Portal veins in tissue sections
The aim of this project is to segment and classify the bile ducts around the portal veins.
Functional analysis of cardiomyocytes derived from pluripotent stem cells
The aim of the project is to study the contractile and electrophysiologic characteristics of cardiomyocytes derived from human induced pluripotent stem cells after exposure to physiological stress and toxic substances. Pluripotent Stem Cells...
IF staining intensity quantification
The project addresses the role of a member of a serine/threonine kinase in pancreatic ductal adenocarcinoma progression
Using bioimage analysis to assess structural & functional responses in the mucosal wall...
Design of an image analysis pipeline which allows for automatic detection of the basal membrane/layer.
Cell morphology quantification
To pursue mechanotransduction research, we have established a polyacrylamide (PAA) gel-based model coating with reconstituted basement membrane (rBM) that allow us to vary the rigidity of the matrix independently of ECM ligand density.
Metabolic regulation of cellular fate in oligodendrocyte precursor cells
The goal is to identify if there are particular time-windows where mitochondria are critical for OPC differentiation and then elucidate the mechanism behind it
Measuring mitochondrial membrane potential using JC-1
Membrane potential has two basic functions. First, it allows a cell to function as a battery, providing power to operate a variety of “molecular devices” embedded in the membrane. Second, in electrically excitable...
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...
Evaluation of a potential genetic driving event in colorectal cancer
Using mouse models we are now exploring its role both during normal intestinal homeostasis and intestinal tumorigenesis
BIK1 localisation thoughout the cell cycle and its function by combining widefield microscopy...
Characterising nuclear BIK1 localisation thoughout the cell cycle and its function by combining widefield microscopy and yeast genetics techniques
3D Colocalization in bovine embryo
Our main aim is to elucidate how lineage specification and pluripotency is controlled in the early embryo
Nucleoplasmic protein localization
To understand how treatments may improve the health- and lifespan of progeroid mice, we assessed the nuclear distribution of various nuclear proteins that play a critical role in the pathophysiology of HGPS, and in particular...
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...
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...
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.
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...
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...
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...
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...
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...
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 ...
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...
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...
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. ...
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...
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...
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...
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...
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...
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......
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...
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 ...
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...
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...
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...