A5037799592- Cell Image Analysis Techniques
- Image Processing Techniques and Applications
- AI in cancer detection
- Medical Image Segmentation Techniques
- Molecular Biology Techniques and Applications
- Innovative Microfluidic and Catalytic Techniques Innovation
- Cardiovascular Disease and Adiposity
- Birth, Development, and Health
- Effects and risks of endocrine disrupting chemicals
- Atherosclerosis and Cardiovascular Diseases
- Per- and polyfluoroalkyl substances research
- Bacterial Identification and Susceptibility Testing
- Lymphatic System and Diseases
- Virus-based gene therapy research
- melanin and skin pigmentation
- Genetics, Bioinformatics, and Biomedical Research
- Adipokines, Inflammation, and Metabolic Diseases
- Image Retrieval and Classification Techniques
- Animal Behavior and Reproduction
- Identification and Quantification in Food
- RNA Interference and Gene Delivery
- Adipose Tissue and Metabolism
- Bladder and Urothelial Cancer Treatments
- Angiogenesis and VEGF in Cancer
- Single-cell and spatial transcriptomics
Information Technology University
2023
Uppsala University
2000-2023
Science for Life Laboratory
2015-2023
Image Intelligence (Sweden)
1995-2018
AstraZeneca (United Kingdom)
2009
Prince of Wales Hospital
2000
UNSW Sydney
2000
University Hospital of North Norway
2000
Abstract Deep Convolutional Neural Networks (DCNN) have recently emerged as superior for many image segmentation tasks. The DCNN performance is however heavily dependent on the availability of large amounts problem-specific training samples. Here we show that DCNNs trained ground truth created automatically using fluorescently labeled cells, perform similar to manual annotations.
Synapses are essential to neural signal transmission. Therefore, quantification of synapses and related neurites from images is vital gain insights into the underlying pathways brain functionality diseases. Despite wide availability synaptic punctum imaging data, several issues impeding satisfactory these structures by current tools. First, antibodies used for labeling not perfectly specific synapses. These may exist in or other cell compartments. Second, brightness different puncta...
It has been observed that immunoreactivity in paraffin sections decreased during storage. In this study, stored from both biopsy material and cultured cells were assessed for changes immunoreactivity, using color-based image analysis to quantitate extent intensity of the stainings. For seven 11 antibodies studied, storage at 20°C 16 weeks reduced immunostaining compared with freshly cut sections. Furthermore, increased temperatures resulted a progressive loss immunoreactivity. After 2...
Abstract Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties single-stranded DNA commonly used RCA-based methods. By introducing a cross-hybridizing oligonucleotide during rolling amplification, we demonstrate that fluorophore-labeled RCA products (RCPs) become smaller. The reduced size RCPs increases local concentration fluorophores and as result, signal intensity together with signal-to-noise ratio....
In this paper, we have developed tools to analyze prokaryotic cells growing in monolayers a microfluidic device. Individual bacterial are identified using novel curvature based approach and tracked over time for several generations. The resulting tracks thereafter assessed filtered on track quality subsequent analysis of growth rates. proposed method performs comparable the state-of-the-art methods segmenting phase contrast fluorescent images, show 10-fold increase speed.
A new method for segmenting images of immunohistochemically stained cell nuclei is presented. The aim to distinguish between with a positive staining reaction and other nuclei, make it possible quantify the reaction. First, supervised algorithm creating pixel classifier applied an image that typical sample. training phase very user friendly since only few pixels each class need be selected. robust in non‐parametric has built‐in metric adapts colour space. After can all from same session....
In this paper we propose an adaptive thresholding method where each object is thresholded optimizing its shape. The based on a component tree representation, which can be computed in quasi-linear time. We test and evaluate the images of bacteria from three different livecell analysis experiments show that proposed produces segmentation results comparable to state-of-the-art but at least order magnitude faster. extended compute any feature measurements calculated cumulative way, holds great...
A fully automatic method for quantification of images immunohistochemically stained cell nuclei by computing area proportions, is presented. Agarose embedded cultured fibroblasts were fixed, paraffin and sectioned at 4 µm. They then together with µm sections the test specimen obtained from bladder cancer material. colour based classifier automatically computed control cells. The was tested on formalin fixed tissue section material, monoclonal antibodies against Ki67 antigen cyclin protein....
Reliable detection and classification of bacteria other pathogens in the human body, animals, food, water is crucial for improving safeguarding public health. For instance, identifying species its antibiotic susceptibility vital effective bacterial infection treatment. Here we show that phase contrast time-lapse microscopy combined with deep learning sufficient to classify four relevant The performed on living does not require fixation or staining, meaning can be determined as reproduce a...
To fully automate intra-abdominal (IAT) and total adipose tissue (TAT) segmentation in mice to replace tedious subjective manual segmentation.A novel transform codes each voxel with the radius of narrowest passage on widest possible three-dimensional (3D) path any target object select appropriate IAT seed points. Then competitive region growing is performed a distance fat mask such that competing classes meet at narrow passages effectively segmenting subcutaneous compartments. Fully...
A method for quantification of images immunohistochemically stained cell nuclei by computing area proportions is presented. The image transformed a principal component transform. resulting first used to segment the objects from background using dynamic thresholding P 2 / ‐histogram, where global roundness measure. Then into hue, defined as angle around component. This positive and negative objects. fully automatic approach makes it robust with respect illumination focus settings. An...
Genital mucosa is the main portal of entry for various incoming pathogens, including human immunodeficiency virus (HIV), hence it an important site host immune defenses. Tissue-resident memory T (TRM) cells defend tissue barriers against infections and are characterized by expression CD103 CD69. In this study, we describe composition CD8+ TRM in ectocervix healthy HIV-infected women. Study samples were collected from Swedish Kenyan uninfected Customized computerized image-based situ analysis...
Abstract In this article, we propose a fast and robust global gray‐level thresholding method based on object size, where the selection of threshold level is recall maximum precision with regard to objects within given size interval. The relies component tree representation, which can be computed in quasi‐linear time. Feature‐based segmentation especially suitable for biomedical microscopy applications often vary number, but have limited variation size. We show that real images cell nuclei...
A wide variety of anthropogenic chemicals is detected in humans and wildlife the health effects various chemical exposures are not well understood. Early life stages generally most susceptible to disruption developmental exposure can cause disease adulthood, but mechanistic understanding such poor. Within EU project EDC-MixRisk, a mixture (Mixture G) was identified Swedish pregnancy cohort SELMA by inverse association between levels women at around gestational week ten with birth weight...
Knowledge on the effects of perfluorohexane sulfonate (PFHxS) ovarian function is limited. In current study, we investigated sensitivity oocytes to PFHxS during in vitro maturation (IVM), including consequences embryo development at morphological, transcriptomic, and epigenomic levels. Bovine cumulus-oocyte complexes (COCs) were exposed 22 h IVM. Following fertilisation, developmental competence was recorded until day 8 culture. Two experiments conducted: 1) exposure COCs 0.01 µg mL-1 − 100...
Abstract Background Hundreds of loci have been robustly associated with circulating lipids, atherosclerosis and coronary artery disease; but for most the causal genes mechanisms remain uncharacterized. Methods We developed a semi-automated experimental pipeline systematic, quantitative, large-scale characterization mechanisms, drugs dyslipidemia in zebrafish model system. validated our using dietary (n>2000), drug treatment (n>1000), genetic intervention (n=384), used it to...
Immunohistochemistry (IHC) in clinical practice is hampered by lack of standardization and subjectivity interpretation quantitation. This study aimed to develop a control system for IHC routinely fixed histoprocessed tissues. Such should be easy handle reflect variations fixation time, section thickness, storage conditions, staining protocols. In addition, image analysis quantitation immunostained tissues, when using classifiers computed on IHC-control images, the very stable. Cultured human...
Abstract Neutral lipids packed in lipid droplets (LDs) are essential as a source of fuel for organisms, and specialized storing cells, the adipocytes, provide buffer energy variations. Many modern‐society‐disorders connected with excess accumulation or deficiency LDs adipose tissue. Intracellular LD number size distribution reflect tissue conditions, while associated mechanisms genes rs still poorly understood. Large‐scale genetic screens using human vitro differentiated primary adipocytes...
Functional validation of candidate genes involved in adaptation and speciation remains challenging. Here, we exemplify the utility a method quantifying individual mRNA transcripts revealing molecular basis divergence feather pigment synthesis during early-stage crows. Using padlock probe assay combined with rolling circle amplification, quantified cell-type-specific gene expression histological context growing follicles. Expression Tyrosinase Related Protein 1 (TYRP1), Solute Carrier Family...