BioImage Informatics

Deep Learning in Image Cytometry: A Review

Gupta A, Harrison PJ, Wieslander H, ..., Sintorn IM, Wählby C

Cytometry - (-) - [2018-12-19; online 2018-12-19]

Image Analysis in Digital Pathology: Combining Automated Assessment of Ki67 Staining Quality with Calculation of Ki67 Cell Proliferation Index

Bengtsson E, Ranefall P

Cytometry - (-) - [2018-12-03; online 2018-12-03]

Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma

Matuszewski DJ, Wählby C, Krona C, Nelander S, Sintorn IM

SLAS DISCOVERY: Advancing Life Sciences R&D - (-) 247255521879141 [2018-08-03; online 2018-08-03]

BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service]

Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103−CD8+ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium

Gibbs A, Buggert M, Edfeldt G, ..., Broliden K, Tjernlund A

- 218 (3) 453-465 [2018-07-02; online 2017-12-20]

Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections

Holzwarth K, Köhler R, Philipsen L, ..., Niesner RA, Hauser AE

Cytometry 93 (9) 876-888 [2018-07-00; online 2018-08-14]

Quantitative image analysis of protein expression and colocalisation in skin sections

Zhang H, Ericsson M, Virtanen M, ..., Vahlquist A, Törmä H

Exp Dermatol 27 (2) 196-199 [2018-02-00; online 2018-01-09]

Whole Slide Image Registration for the Study of Tumor Heterogeneity

Solorzano L, Almeida GM, Mesquita B, ..., Oliveira C, Wählby C

- - (-) 95-102 [2018-00-00; online 2018-09-14]

Year 2017

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

Sadanandan SK, Ranefall P, Le Guyader S, Wählby C

Sci Rep 7 (1) - [2017-12-00; online 2017-08-10]

A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

Carreras-Puigvert J, Zitnik M, Jemth AS, ..., Zupan B, Helleday T

Nat Commun 8 (1) - [2017-12-00; online 2017-11-16]

BioImage Informatics [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF) [Service]

A short feature vector for image matching: The Log-Polar Magnitude feature descriptor

Matuszewski DJ, Hast A, Wählby C, Sintorn IM

PLoS ONE 12 (11) e0188496 [2017-11-30; online 2017-11-30]

Deep Convolutional Neural Networks For Detecting Cellular Changes Due To Malignancy

Wieslander H, Forslid G, Bengtsson E, ..., Runow Stark C, Kecheril Sadanandan S

The IEEE International Conference on Computer Vision (ICCV), 2017 - (-) - [2017-11-01; online 2017-09-13]

Highly HIV-exposed HIV uninfected Kenyan female sex workers display a thick ectocervical epithelium

Röhl M, Lajoie J, Tjernlund A, ..., Fowke KR, Broliden K

HIV&Hepatitis Nordic Conference, Stockholm, 2017-09-27-29 - (-) - [2017-11-01]

Spheroid segmentation using multiscale deep adversarial networks

Kecheril Sadanandan S, Karlsson J, Wählby C

The IEEE International Conference on Computer Vision (ICCV), 2017 - (-) 36-41 [2017-11-01; online 2017-09-13]

Zebrafish larvae as a model system for high-throughput, image-based screens in diabetes and insulin resistance

Emmanouilidou A, Ranefall P, Bandaru M, ..., Ingelsson E, den Hoed M

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

Zebrafish larvae as a model system for high-throughput, image-based genetic screens in cardiometabolic diseases

den Hoed M, Emmanouilidou A, Bandaru M, ..., Larsson A, Ingelsson E

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

Identifying and characterizing causal genes in GWAS-identified loci for heart rate variability using high-throughput, image-based screens in zebrafish larvae

von der Heyde B, Emmanouilidou A, Klingström T, ..., Allalou A, den Hoed M

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

Large-scale validation of zebrafish larvae as a model system for genetic screens in dyslipidaemia, atherosclerosis and coronary artery disease

Bandaru M, Emmanouilidou A, Ranefall P, ..., Ingelsson E, den Hoed M

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

Quantitative high-content/high-throughput microscopy analysis of lipid droplets in subject-specific adipogenesis models

Bombrun M, Gao H, Ranefall P, ..., Arner P, Wählby C

Cytometry - (-) - [2017-10-14; online 2017-10-14]

Hormonal contraceptive use affects HIV susceptibility: mechanisms revealed by image analysis

Edfeldt G, Röhl M, Lajoie J, ..., Fowke KR, Broliden K

HIV&Hepatitis Nordic Conference, Stockholm, 2017-09-27-29 - (-) - [2017-09-27]

HIV-infected women have high numbers of CD103-CD8+ T cells residing close to the basal membrane of the ectocervical epithelium

PubMed

Tjernlund A, Gibbs A, Buggert M, ..., Wählby C, Broliden K

HIV&Hepatitis Nordic Conference, Stockholm, 2017-09-27-29 - (-) - [2017-09-27]

Objective automated quantification of fluorescence signal in histological sections of rat lens

Talebizadeh N, Hagström NZ, Yu Z, ..., Söderberg P, Wählby C

Cytometry 91 (8) 815-821 [2017-08-00; online 2017-05-11]

Multi-label prediction of subcellular localization in confocal images using deep neural networks

Winsnes CF, Sullivan DP, Smith K, Lundberg E

Molecular Biology of the Cell 27 (-) - [2017-04-10; online 2017-04-10]

Analysis of the distribution of CD103 on CD8 T cells in blood and genital mucosa of HIV-infected female sex workers

Gibbs A, Buggert M, Ranefall P, ..., Broliden K, Tjernlund A

AIDS Research and Human Retroviruses 32 (S1) 307 [2017-01-24]

Deep Fish: Deep Learning–Based Classification of Zebrafish Deformation for High-Throughput Screening

Ishaq O, Sadanandan SK, Wählby C

SLAS DISCOVERY: Advancing Life Sciences R&D 22 (1) 102-107 [2017-01-00; online 2016-09-26]

Decoding Gene Expression in 2D and 3D

Bombrun M, Ranefall P, Lindblad J, ..., Nilsson M, Wählby C

Scandinavian Conference on Image Analysis 2017 - (-) 257-268 [2017-00-00; online 2017-05-19]

Differential Neuroprotective Effects of Interleukin-1 Receptor Antagonist on Spinal Cord Neurons after Excitotoxic Injury

Schizas N, Perry S, Andersson B, ..., Kullander K, Hailer NP

Neuroimmunomodulation 24 (4-5) 220-230 [2017-00-00; online 2018-01-26]

Analysis of the Distribution of CD103 on CD8 T Cells in Blood and Genital Mucosa of HIVinfected Female Sex Workers

Year 2016

Gibbs A, Buggert M, Ranefall P, ..., Broliden K, Tjernlund A

Conference on HIV Research for Prevention (HIV R4P), 2016, October 17–20, Chicago - (-) - [2016-10-17]

Global gray-level thresholding based on object size.

Ranefall P, Wählby C

Cytometry A 89 (4) 385-390 [2016-04-00; online 2016-01-23]

PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data

Matuszewski DJ, Wählby C, Puigvert JC, Sintorn IM

PLoS ONE 11 (3) e0151554 [2016-03-17; online 2016-03-17]

Segmentation and Track-Analysis in Time-Lapse Imaging of Bacteria

Sadanandan SK, Baltekin O, Magnusson KEG, ..., Elf J, Wahlby C

IEEE J. Sel. Top. Signal Process. 10 (1) 174-184 [2016-02-00; online 2016-02-00]

Feature Augmented Deep Neural Networks for Segmentation of Cells

Sadanandan SK, Ranefall P, Wählby C

- - (-) 231-243 [2016-00-00; online 2016-09-18]

Bridging Histology and Bioinformatics—Computational Analysis of Spatially Resolved Transcriptomics

Mignardi M, Ishaq O, Qian X, Wahlby C

Proc. IEEE - (-) 1-12 [2016-00-00; online 2016-00-00]

Year 2015

Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio.

Clausson C, Arngården L, Ishaq O, ..., Wählby C, Söderberg O

pmc

Sci Rep 5 (-) 12317 [2015-07-23; online 2015-07-23]

Advanced Light Microscopy (ALM) [Collaborative] BioImage Informatics [Technology development]

Year 2013

Automated classification of immunostaining patterns in breast tissue from the human protein atlas.

Swamidoss IN, Kårsnäs A, Uhlmann V, ..., Wählby C, Strand R

pmc

J Pathol Inform 4 (Suppl) S14 [2013-03-30; online 2013-03-30]

BioImage Informatics [Technology development] Tissue Profiling

Year 2012

Visualising individual sequence-specific protein-DNA interactions in situ.

Weibrecht I, Gavrilovic M, Lindbom L, ..., Wählby C, Söderberg O

N Biotechnol 29 (5) 589-598 [2012-06-15; online 2011-09-13]

BioImage Informatics [Collaborative] PLA Proteomics

Year 2011