Petter Ranefall
Bioinformatician at Institutionen för informationsteknologi; Vi3; Bildanalys
- E-mail:
- petter.ranefall@it.uu.se
- Visiting address:
- Hus 10, Lägerhyddsvägen 1
- Postal address:
- Box 337
751 05 UPPSALA
- CV:
- Download CV
- ORCID:
- 0000-0002-6699-4015
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Short presentation
I am Docent in Computerized Image Processing and employed by SciLifeLab as an image analysis resource. My job is to help researchers getting started analysing their images. The aim is primarily to set up pipelines that the partners can apply themselves. It is often good to discuss suitable prerequisites for the imaging, already before all images are acquired.
SciLifeLab BioImage Informatics web page: www.scilifelab.se/facilities/bioimage-informatics/
Personal web page: user.it.uu.se/~peran517/
Keywords
- bioimage informatics
- image analysis
- quantitative microscopy
- scilifelab
Publications
Selection of publications
- Compaction of rolling circle amplification products increases signal integrity and signal–to–noise ratio (2015)
- Large-Scale Analysis of Cells and Tissue (2014)
- The Giga-pixel Challenge: Full Resolution Image Analysis – Without Losing the Big Picture (2014)
- Towards Automatic Quantification of Immunohistochemistry Using Colour Image Analysis (1998)
Recent publications
- Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy (2023)
- RegiSTORM (2023)
- mafba and mafbb differentially regulate lymphatic endothelial cell migration in topographically distinct manners (2022)
- Bovine oocyte exposure to perfluorohexane sulfonate (PFHxS) induces phenotypic, transcriptomic, and DNA methylation changes in resulting embryos in vitro (2022)
- Occurrence of late-apoptotic symptoms in porcine preimplantation embryos upon exposure of oocytes to perfluoroalkyl substances (PFASs) under in vitro meiotic maturation (2022)
All publications
Articles
- Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy (2023)
- RegiSTORM (2023)
- mafba and mafbb differentially regulate lymphatic endothelial cell migration in topographically distinct manners (2022)
- Bovine oocyte exposure to perfluorohexane sulfonate (PFHxS) induces phenotypic, transcriptomic, and DNA methylation changes in resulting embryos in vitro (2022)
- Occurrence of late-apoptotic symptoms in porcine preimplantation embryos upon exposure of oocytes to perfluoroalkyl substances (PFASs) under in vitro meiotic maturation (2022)
- Mafba and Mafbb Differentially Regulate Lymphatic Endothelial Cell Migration in Topographically Distinct Manners (2021)
- Increased apoptosis, reduced Wnt/β-catenin signaling, and altered tail development in zebrafish embryos exposed to a human-relevant chemical mixture (2021)
- A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures (2020)
- SynQuant (2020)
- Image analysis in digital pathology (2019)
- In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation (2019)
- Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103-CD8+ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium (2018)
- Quantitative high-content/high-throughput microscopy analysis of lipid droplets in subject-specific adipogenesis models (2017)
- Increased numbers of CD103-CD8+ TRM cells in the cervical mucosa of HIV-infected women (2017)
- Automated training of deep convolutional neural networks for cell segmentation (2017)
- Analysis of the distribution of CD103 on CD8 T cells in blood and genital mucosa of HIV-infected female sex workers (2016)
- Segmentation and track-analysis in time-lapse imaging of bacteria (2016)
- Global Gray-level Thresholding Based on Object Size (2016)
- Compaction of rolling circle amplification products increases signal integrity and signal–to–noise ratio (2015)
- Cultured human fibroblasts in agarose gel as a multi-functional controlfor immunohistochemistry. Standardization Of Ki67 (MIB1) assessment inroutinely processed urinary bladder carcinoma tissue. (2000)
- Paraffin section storage and immunohistochemistry. Effects of time,temperature, fixation, and retrieval protocol with emphasis on p53 proteinand MIB1 antigen. (2000)
- Paraffin section storage and immunohistochemistry - Effects of time, temperature, fixation, and retrieval protocol with emphasis on p53 protein and MIB1 antigen (2000)
- Cultured human fibroblasts in agarose gel as a multi-functional control for immunohistochemistry (2000)
- Automatic quantification of microvessel density in urinary bladdercarcinoma. (1999)
- Automatic quantification of microvessel density in urinary bladder carcinoma (1999)
- Automatic quantification of immunohistochemically stained cell nuclei based on standard reference cells (1998)
- Automatic quantification of immunohistochemically stained cell nuclei using unsupervised image analysis (1998)
- Automatic quantification of microvessels using unsupervised image analysis. (1998)
- Automatic quantification of microvessels using unsupervised image analysis (1998)
- A Deformable Atlas of the Chest Based on the Visible Man (1998)
- Effect of androgen deprivation on epithelial and mesenchymal tissue components in localized prostate cancer (1997)
- A new method for segmentation of colour images applied on immunohistochemically stained cells. (1997)
- A new method for segmentation of colour images applied to immunohistochemically stained cell nuclei (1997)
- A New Method for Creating a Pixelwise Box classifier for Colour Images (1997)
Books
Conferences
- Learning Cell Nuclei Segmentation Using Labels Generated with Classical Image Analysis Methods (2021)
- Decoding gene expression in 2D and 3D (2017)
- A web application to analyse and visualize digital images at multiple resolutions (2017)
- TissueMaps (2016)
- Feature augmented deep neural networks for segmentation of cells (2016)
- Fast Adaptive Local Thresholding Based on Ellipse fit (2016)
- Global And Local Adaptive Gray-level Thresholding Based on Object Features (2016)
- Automatic grading of breast cancer from whole slide images of Ki67 stained tissue sections (2016)
- Your New Default Thresholding Method? (2015)
- Large-Scale Analysis of Cells and Tissue (2014)
- The Giga-pixel Challenge: Full Resolution Image Analysis – Without Losing the Big Picture (2014)
- Viewing and analyzing slide scanner data using CellProfiler (work in progress) (2013)
- Finding Facial Features Using an HLS Colour Space (1995)
Other
