BioImage Informatics

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SciLifeLab Infrastructure Unit since 2016.

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2016

Ended: Current

Year 2024

PubMed DOI Crossref
Liver X receptor unlinks intestinal regeneration and tumorigenesis.
Das S, Parigi SM, Luo X, ..., Katajisto P, Villablanca EJ
Nature - (-) - [2024-11-20; online 2024-11-20]
BioImage Informatics [Service] Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
High-parametric protein maps reveal the spatial organization in early-developing human lung.
Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B
Nat Commun 15 (1) 9381 [2024-10-30; online 2024-10-30]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
The crucial role of bioimage analysts in scientific research and publication.
Cimini BA, Bankhead P, D'Antuono R, ..., Wiggins L, Eliceiri KW
J. Cell. Sci. 137 (20) - [2024-10-15; online 2024-10-30]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Integrated Microscopy Technologies Gothenburg [Service]
PubMed DOI Crossref
Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim.
Andersson A, Escriva Conde M, Surova O, ..., Nilsson M, Nyström H
Clin. Cancer Res. 30 (19) 4517-4529 [2024-10-01; online 2024-07-26]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] In Situ Sequencing (ISS) [Service]
PubMed DOI Crossref
Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data.
Andersson A, Behanova A, Avenel C, ..., Malmberg F, Wählby C
Cytometry A 105 (9) 677-687 [2024-09-00; online 2024-07-03]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
Making Multiplexed Imaging Flexible: Combining Essential Markers With Established Antibody Panels.
Deen AJ, Thorsson J, O'Roberts EM, ..., Oses C, Stadler C
J. Histochem. Cytochem. 72 (8-9) 517-544 [2024-08-31; online 2024-08-31]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] Spatial Proteomics [Technology development]
PubMed DOI Crossref
Multiple cis-regulatory elements control prox1a expression in distinct lymphatic vascular beds.
Panara V, Yu H, Peng D, ..., Hogan BM, Koltowska K
Development 151 (9) - [2024-05-01; online 2024-05-09]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
PubMed DOI Crossref
Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology.
Kukanja P, Langseth CM, Rubio Rodríguez-Kirby LA, ..., Nilsson M, Castelo-Branco G
Cell 187 (8) 1990-2009.e19 [2024-04-11; online 2024-03-20]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.
ElBeck Z, Hossain MB, Siga H, ..., Végvári Á, Betsholtz C
Nat Commun 15 (1) 2358 [2024-03-20; online 2024-03-20]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling.
Bivehed E, Hellman B, Wenson L, ..., Söderberg O, Heldin J
Nucleic Acids Res. 52 (4) e22 [2024-02-28; online 2024-01-23]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
DOI Crossref
Vaginal candida infection is associated with host molecular signatures of neutrophil activation in the adjacent ectocervical mucosa in Kenyan sex workers
Hasselrot T, Boger MF, Kaldhusdal V, ..., Czarnewski P, Broliden K
American J Rep Immunol 91 (2) - [2024-02-00; online 2024-01-31]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Year 2023

PubMed DOI Crossref
An end-to-end workflow for multiplexed image processing and analysis.
Windhager J, Zanotelli VRT, Schulz D, ..., Bodenmiller B, Eling N
Nat Protoc - (-) - [2023-10-10; online 2023-10-10]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
PubMed DOI Crossref
Tailoring vascular phenotype through AAV therapy promotes anti-tumor immunity in glioma.
Ramachandran M, Vaccaro A, van de Walle T, ..., Essand M, Dimberg A
Cancer Cell 41 (6) 1134-1151.e10 [2023-06-12; online 2023-05-11]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
PubMed DOI Crossref
RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy.
Øvrebø Ø, Ojansivu M, Kartasalo K, ..., Holme MN, Stevens MM
BMC Bioinformatics 24 (1) 237 [2023-06-05; online 2023-06-05]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
A topical rectal douche product containing Q-Griffithsin does not disrupt the epithelial border or alter CD4+ cell distribution in the human rectal mucosa.
Franzén Boger M, Benhach N, Hasselrot T, ..., Broliden K, Tjernlund A
Sci Rep 13 (1) 7547 [2023-05-09; online 2023-05-09]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
PubMed DOI Crossref
TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data.
Pielawski N, Andersson A, Avenel C, ..., Solorzano L, Wählby C
Heliyon 9 (5) e15306 [2023-05-00; online 2023-04-17]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.
Li X, Andrusivova Z, Czarnewski P, ..., Lundeberg J, Sundström E
Nat. Neurosci. 26 (5) 891-901 [2023-05-00; online 2023-04-24]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Collaborative] NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High-content analysis shows synergistic effects of low perfluorooctanoic acid (PFOS) and perfluorooctane sulfonic acid (PFOA) mixture concentrations on human breast epithelial cell carcinogenesis.
Pierozan P, Kosnik M, Karlsson O
Environ Int 172 (-) 107746 [2023-02-00; online 2023-01-12]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.
Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C
Nat Cell Biol 25 (2) 351-365 [2023-02-00; online 2023-01-16]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] In Situ Sequencing (ISS) [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3
Behanova A, Avenel C, Andersson A, ..., Östman A, Wählby C
Biol. Imaging 3 (-) - [2023-00-00; online 2023-02-20]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Year 2022

PubMed DOI Crossref
A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint.
Leyhr J, Waldmann L, Filipek-Górniok B, ..., Allalou A, Haitina T
Elife 11 (-) - [2022-11-15; online 2022-11-15]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
PubMed DOI Crossref
The role of Gdf5 in the development of the zebrafish fin endoskeleton.
Waldmann L, Leyhr J, Zhang H, ..., Öhman-Mägi C, Haitina T
Dev. Dyn. 251 (9) 1535-1549 [2022-09-00; online 2021-07-29]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
Automated detection of vascular remodeling in tumor-draining lymph nodes by the deep-learning tool HEV-finder.
Bekkhus T, Avenel C, Hanna S, ..., Wählby C, Ulvmar MH
J. Pathol. 258 (1) 4-11 [2022-09-00; online 2022-07-12]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
A method for Boolean analysis of protein interactions at a molecular level.
Raykova D, Kermpatsou D, Malmqvist T, ..., Kampf C, Söderberg O
Nat Commun 13 (1) 4755 [2022-08-13; online 2022-08-13]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images.
Gupta A, Sabirsh A, Wahlby C, Sintorn IM
IEEE J Biomed Health Inform 26 (8) 4079-4089 [2022-08-00; online 2022-08-11]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.
Marco Salas S, Yuan X, Sylven C, ..., Wählby C, Partel G
PLoS Comput. Biol. 18 (8) e1010366 [2022-08-00; online 2022-08-12]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] In Situ Sequencing (ISS) [Collaborative]
PubMed DOI Crossref
A Hitchhiker's guide through the bio-image analysis software universe.
Haase R, Fazeli E, Legland D, ..., Klemm A, Tischer C
FEBS Lett. - (-) - [2022-07-14; online 2022-07-14]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
mafba and mafbb differentially regulate lymphatic endothelial cell migration in topographically distinct manners.
Arnold H, Panara V, Hußmann M, ..., Schulte-Merker S, Koltowska K
Cell Rep 39 (12) 110982 [2022-06-21; online 2022-06-23]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
The microtubule plus-end tracking protein Bik1 is required for chromosome congression.
Julner A, Abbasi M, Menéndez-Benito V
Mol. Biol. Cell 33 (5) br7 [2022-05-01; online 2022-03-02]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
PubMed DOI Crossref
Multi-omics analysis of the cervical epithelial integrity of women using depot medroxyprogesterone acetate.
Bradley F, Franzén Boger M, Kaldhusdal V, ..., Tjernlund A, Broliden K
PLoS Pathog. 18 (5) e1010494 [2022-05-00; online 2022-05-09]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Bovine oocyte exposure to perfluorohexane sulfonate (PFHxS) induces phenotypic, transcriptomic, and DNA methylation changes in resulting embryos in vitro.
Hallberg I, Persson S, Olovsson M, ..., Rüegg J, Sjunnesson YCB
Reprod Toxicol 109 (-) 19-30 [2022-04-00; online 2022-02-24]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development.
Habicher J, Varshney GK, Waldmann L, ..., Burgess SM, Ledin J
PLoS Genet. 18 (2) e1010067 [2022-02-00; online 2022-02-22]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
Spatial Statistics for Understanding Tissue Organization.
Behanova A, Klemm A, Wählby C
Front Physiol 13 (-) 832417 [2022-01-28; online 2022-01-28]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
An Image-Analysis-Based Method for the Prediction of Recombinant Protein Fiber Tensile Strength.
Bäcklund FG, Schmuck B, Miranda GHB, ..., Rydén J, Rising A
Materials (Basel) 15 (3) - [2022-01-18; online 2022-01-18]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
Improved breast cancer histological grading using deep learning.
Wang Y, Acs B, Robertson S, ..., Hartman J, Rantalainen M
Ann. Oncol. 33 (1) 89-98 [2022-01-00; online 2021-09-29]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service]
DOI Crossref
Batch Processing Methods in ImageJ
Klemm A, Miura K
Springer - (-) 7-27 [2022-00-00; online 2022-09-29]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Year 2021

PubMed DOI Crossref
Perfluorooctane sulfonate (PFOS) exposure of bovine oocytes affects early embryonic development at human-relevant levels in an in vitro model.
Hallberg I, Persson S, Olovsson M, ..., Rüegg J, Sjunnesson YCB
Toxicology 464 (-) 153028 [2021-12-00; online 2021-11-08]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
PubMed DOI Crossref
Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer.
Chelebian E, Avenel C, Kartasalo K, ..., Lundeberg J, Wählby C
Cancers (Basel) 13 (19) - [2021-09-28; online 2021-09-28]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
The broad role of Nkx3.2 in the development of the zebrafish axial skeleton.
Waldmann L, Leyhr J, Zhang H, ..., Allalou A, Haitina T
PLoS ONE 16 (8) e0255953 [2021-08-19; online 2021-08-19]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
Machine learning for cell classification and neighborhood analysis in glioma tissue.
Solorzano L, Wik L, Olsson Bontell T, ..., Östman A, Wählby C
Cytometry A - (-) - [2021-06-04; online 2021-06-04]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis.
Dobson ETA, Cimini B, Klemm AH, ..., Carpenter AE, Eliceiri KW
Curr Protoc 1 (5) e89 [2021-05-00; online 2021-05-27]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists.
Martins GG, Cordelières FP, Colombelli J, ..., Tinevez JY, Miura K
F1000Res 10 (-) 334 [2021-04-30; online 2021-04-30]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
Bioimage analysis workflows: community resources to navigate through a complex ecosystem.
Paul-Gilloteaux P, Tosi S, Hériché JK, ..., Miura K, Colombelli J
F1000Res 10 (-) 320 [2021-04-26; online 2021-04-26]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
Increased apoptosis, reduced Wnt/β-catenin signaling, and altered tail development in zebrafish embryos exposed to a human-relevant chemical mixture.
Smirnova A, Mentor A, Ranefall P, ..., Mattsson A, Jönsson M
Chemosphere 264 (1) 128467 [2021-02-00; online 2020-09-30]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
Acute systemic LPS-exposure impairs perivascular CSF distribution in mice.
Manouchehrian O, Ramos M, Bachiller S, Lundgaard I, Deierborg T
J Neuroinflammation 18 (1) 34 [2021-01-29; online 2021-01-29]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
DOI Crossref
Learning Cell Nuclei Segmentation Using Labels Generated With Classical Image Analysis Methods
Matuszewski DJ, Ranefall P
- - (-) - [2021-00-00; online 2021-00-00]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Year 2020

DOI Crossref
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]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
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]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
Automated identification of the mouse brain's spatial compartments from in situ sequencing data.
Partel G, Hilscher MM, Milli G, ..., Nilsson M, Wählby C
BMC Biol. 18 (1) 144 [2020-10-19; online 2020-10-19]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
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
J. Infect. Dis. - (-) - [2020-08-11; online 2020-08-11]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
PubMed DOI Crossref
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
Biomed. Opt. Express 11 (8) 4290-4305 [2020-08-01; online 2020-07-15]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development] Bioinformatics Support for Computational Resources [Service] Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
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 [2020-07-16; online 2020-07-16]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] 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]
DOI Crossref
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
Behavioral Characterization of dmrt3a Mutant Zebrafish Reveals Crucial Aspects of Vertebrate Locomotion through Phenotypes Related to Acceleration.
Del Pozo A, Manuel R, Iglesias Gonzalez AB, ..., Kullander K, Boije H
eNeuro 7 (3) ENEURO.0047-20.2020 [2020-05-18; online 2020-05-18]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] Bioinformatics Support for Computational Resources [Service] Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
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
Lancet Oncol 21 (2) 222-232 [2020-02-00; online 2020-01-08]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] Bioinformatics Support for Computational Resources [Service]

Year 2019

PubMed DOI Crossref
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
Sci Rep 9 (1) 18120 [2019-12-02; online 2019-12-02]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
PubMed DOI Crossref
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 [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
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 [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
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 M
Sci Rep 9 (1) 10730 [2019-07-24; online 2019-07-24]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] Genome Engineering Zebrafish [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Image Analysis in Digital Pathology: Combining Automated Assessment of Ki67 Staining Quality with Calculation of Ki67 Cell Proliferation Index.
Bengtsson E, Ranefall P
Cytometry A 95 (7) 714-716 [2019-07-00; online 2018-12-03]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
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]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
Deep Learning in Image Cytometry: A Review.
Gupta A, Harrison PJ, Wieslander H, ..., Sintorn IM, Wählby C
Cytometry A 95 (4) 366-380 [2019-04-00; online 2018-12-19]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation.
Wu C, Klaesson A, Buskas J, ..., Söderberg O, Wolf JBW
J Exp Biol 222 (Pt 5) jeb194431 [2019-03-08; online 2019-03-08]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service]

Year 2018

PubMed DOI Crossref
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 23 (10) 1030-1039 [2018-12-00; online 2018-08-03]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
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 [2018-10-00; online 2018-10-01]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Spatial Proteomics [Collaborative]
PubMed DOI Crossref
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
J. Infect. Dis. 218 (3) 453-465 [2018-07-02; online 2017-12-23]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
DOI Crossref
Abstract 472: Identifying and Characterizing Causal Genes in GWAS-identified Loci for Triglyceride Levels Using High-throughput, Image-based Screens in Zebrafish Larvae
von der Heyde B, Masiero M, Emmanouilidou A, Klingström T, den Hoed M
Arterioscler. Thromb. Vasc. Biol. 38 (Suppl_1) - [2018-05-00; online 2018-05-00]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
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]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
DOI Crossref
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]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Year 2017

PubMed DOI Crossref
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]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
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] Bioinformatics (NBIS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
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]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
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 A 91 (11) 1068-1077 [2017-11-00; online 2017-10-14]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
DOI Crossref
Spheroid Segmentation Using Multiscale Deep Adversarial Networks
Sadanandan SK, Karlsson J, Wahlby C
The IEEE International Conference on Computer Vision (ICCV), 2017 - (-) 36-41 [2017-10-00; online 2017-10-00]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
Hormonal contraceptive use affects HIV susceptibility: mechanisms revealed by image analysis
Edfeldt G , Lajoie J , Röhl M , Tjernlund A
Scand J Immunol 86 (4) 249-350 [2017-10-00; online 2017-09-27]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
DOI Crossref
Deep Convolutional Neural Networks for Detecting Cellular Changes Due to Malignancy
Forslid G, Wieslander H, Bengtsson E, ..., Stark CR, Sadanandan SK
The IEEE International Conference on Computer Vision (ICCV), 2017 - (-) - [2017-10-00; online 2017-10-00]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
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]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
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]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
DOI Crossref
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Year 2016

Analysis of the Distribution of CD103 on CD8 T Cells in Blood and Genital Mucosa of HIVinfected Female Sex Workers
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
Abstracts of the HIV Research for Prevention Meeting, HIVR4P, 17-20 October, 2016, Chicago, USA
AIDS Research and Human Retroviruses 32 (S1) 1-409 [2016-10-00; online 2016-10-00]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
PubMed DOI Crossref
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]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
PubMed DOI Crossref
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]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service]
DOI Crossref
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]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
DOI Crossref
Feature Augmented Deep Neural Networks for Segmentation of Cells
Sadanandan SK, Ranefall P, Wählby C
- - (-) 231-243 [2016-00-00; online 2016-09-18]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]
DOI Crossref
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Year 2015

PubMed DOI Crossref
Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio.
Clausson C, Arngården L, Ishaq O, ..., Wählby C, Söderberg O
Sci Rep 5 (-) 12317 [2015-07-23; online 2015-07-23]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development] Integrated Microscopy Technologies Stockholm [Collaborative]

Year 2013

PubMed DOI Crossref
Automated classification of immunostaining patterns in breast tissue from the human protein atlas.
Swamidoss IN, Kårsnäs A, Uhlmann V, ..., Wählby C, Strand R
J Pathol Inform 4 (Suppl) S14 [2013-03-30; online 2013-03-30]
BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development] Tissue Profiling

Year 2012

PubMed DOI Crossref
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]
Affinity Proteomics Uppsala [Collaborative] BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] PLA and Single Cell Proteomics

Year 2011

PubMed DOI Crossref
Increasing the dynamic range of in situ PLA.
Clausson C, Allalou A, Weibrecht I, ..., Wählby C, Söderberg O
Nat. Methods 8 (11) 892-893 [2011-10-28; online 2011-10-28]
Affinity Proteomics Uppsala [Collaborative] BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] PLA and Single Cell Proteomics
SciLifeLab Data Centre
Publications 9.5.1