Wählby C

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Family name Wählby
Given name Carolina
Initials C
ORCID

ORCID 0000-0002-4139-7003
Affiliations Centre for Image AnalysisUppsala University Uppsala 75124 Sweden
BioImage Informatics Facility of SciLifeLab Uppsala 75124 Sweden

44 publications

PubMed DOI Crossref
Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.
Marco Salas S, Kuemmerle LB, Mattsson-Langseth C, ..., Ishaque N, Nilsson M
Nat. Methods 22 (4) 813-823 [2025-04-00; online 2025-03-13]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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 [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]
DOI Crossref
Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows
Salas SM, Czarnewski P, Kuemmerle LB, ..., Ishaque N, Nilsson M
- - (-) - [2023-02-14; online 2023-02-14]
In Situ Sequencing [Technology development]
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
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 [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]
DOI Crossref
Developmental origins of cell heterogeneity in the human lung
Sountoulidis A, Salas SM, Braun E, ..., Nilsson M, Samakovlis C
- - (-) - [2022-01-12; online 2022-01-12]
In Situ Sequencing [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
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
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
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]
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
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]
DOI Crossref
Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis
Bandaru MK, Emmanouilidou A, Ranefall P, ..., Ingelsson E, den Hoed M
- - (-) - [2018-12-20; online 2018-12-20]
Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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
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]
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]
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 [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 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
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]
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]
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]
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]
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]
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]
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
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]
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]
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
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
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