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...

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...

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...

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...

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...

An image-based analysis of recombinant silk fiber structures

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

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.

IF staining intensity quantification

IF staining intensity quantification

The project addresses the role of a member of a serine/threonine kinase in pancreatic ductal adenocarcinoma progression

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.

Cell morphology quantification

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

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

Measuring mitochondrial membrane potential using JC-1

Project Description 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

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

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 and yeast genetics techniques

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

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

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 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 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...

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.