BioImage Informatics

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

von der Heyde B, Emmanouilidou A, Mazzaferro E, ..., Brooke HL, den Hoed M

Sci Rep 10 (1) 11831 [2020-12-00; online 2020-07-16]

BioImage Informatics Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Genome Engineering Zebrafish [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]

A workflow for high-throughput screening, data analysis, processing, and hit identification

Hansel CS, Yousefian S, Klemm AH, Carreras-Puigvert J

KNIME blog https://www.knime.com/blog/a-workflow-for-high-throughput-screening-data-analysis-processing-and-hit-identification (-) - [2020-11-30; online 2020-06-19]

TrackMate: My favorite image analysis tool, by Neubias members

Klemm A

Wiley Analytical Science https://analyticalscience.wiley.com/do/10.1002/was.000400044 (-) - [2020-11-30; online 2020-05-26]

Automated identification of the mouse brain's spatial compartments from in situ sequencing data.

Partel G, Hilscher MM, Milli G, ..., Nilsson M, Wählby C

pii: 10.1186/s12915-020-00874-5 pmc: PMC7574211

BMC Biol. 18 (1) 144 [2020-10-19; online 2020-10-19]

BioImage Informatics Bioinformatics Compute and Storage [Service]

Regular use of depot medroxyprogesterone acetate causes thinning of the superficial lining and apical distribution of HIV target cells in the human ectocervix.

Edfeldt G, Lajoie J, Röhl M, ..., Broliden K, Tjernlund A

pii: 5891260

J. Infect. Dis. - (-) - [2020-08-11; online 2020-08-11]

BioImage Informatics

zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.

Zhang H, Waldmann L, Manuel R, ..., Haitina T, Allalou A

pii: 393519 pmc: PMC7449731

Biomed. Opt. Express 11 (8) 4290-4305 [2020-08-01; online 2020-07-15]

BioImage Informatics Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Adding seemingly uninformative labels helps in low data regimes

Matsoukas C, Hernandez A, Liu Y, ..., Strand F, Smith K

International Conference on Machine Learning (ICML) - (-) - [2020-07-15]

Behavioural characterization of dmrt3a mutant zebrafish reveals crucial aspects of vertebrate locomotion through phenotypes related to acceleration

del Pozo Cano A, Manuel R, Iglesias Gonzalez AB, ..., Kullander K, Boije H

eNeuro 7 (3) ENEURO.0047-20.2020 [2020-05-01; online 2020-05-01]

BioImage Informatics Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study.

Ström P, Kartasalo K, Olsson H, ..., Egevad L, Eklund M

pii: S1470-2045(19)30738-7

Lancet Oncol 21 (2) 222-232 [2020-02-00; online 2020-01-08]

BioImage Informatics Bioinformatics Compute and Storage [Service]

Year 2019

Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa.

Günaydın G, Edfeldt G, Garber DA, ..., Tjernlund A, Broliden K

pii: 10.1038/s41598-019-54493-4

Sci Rep 9 (1) 18120 [2019-12-02; online 2019-12-02]

TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish

Gudmundsson S, Wilbe M, Filipek-Górniok B, ..., Annerén G, Bondeson ML

Sci Rep 9 (1) - [2019-12-00; online 2019-07-24]

BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] Genome Engineering Zebrafish [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures: Two image analytic approaches using adaptive thresholds or machine learning

Ossinger A, Bajic A, Pan S, ..., Hailer NP, Schizas N

Journal of Neuroscience Methods 331 (-) 108522 [2019-11-00; online 2019-11-00]

BioImage Informatics Bioinformatics Compute and Storage [Service]

SynQuant: an automatic tool to quantify synapses from microscopy images

Wang Y, Wang C, Ranefall P, ..., Tian L, Yu G

Bioinformatics 36 (5) 1599-1606 [2019-10-09; online 2019-10-09]

BioImage Informatics

Tracking Microscope Performance: A Workflow to Compare Point Spread Function Evaluations Over Time

Klemm AH, Thomae AW, Wachal K, Dietzel S

Microsc Microanal 25 (3) 699-704 [2019-06-00; online 2019-02-06]

In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation

Wu CC, Klaesson A, Buskas J, ..., Söderberg O, Wolf JBW

J Exp Biol 222 (5) jeb194431 [2019-03-01; online 2019-02-04]

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

Year 2018

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]

Deep learning is combined with massive-scale citizen science to improve large-scale image classification

Sullivan DP, Winsnes CF, Åkesson L, ..., Szantner A, Lundberg E

Nat Biotechnol 36 (9) 820-828 [2018-08-20; online 2018-08-20]

BioImage Informatics [Collaborative] Cell Profiling [Collaborative]

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

cb.uu.se: http://www.cb.uu.se/~carolina/timelapse_data/ data.broadinstitute.org: https://data.broadinstitute.org/bbbc/BBBC022/

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

cb.uu.se: http://cb.uu.se/~damian/LPM.html

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

cb.uu.se: http://www.cb.uu.se/~petter/downloads/CellClusters/ cb.uu.se: http://www.cb.uu.se/~petter/downloads/SIP/ murphylab.web.cmu.edu: http://murphylab.web.cmu.edu/data/2009_ISBI_Nuclei.html smal.we: http://smal.ws/wp/software/synthetic-data-generator/

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]