Wählby C

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] In Situ Sequencing (ISS) [Service]

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]

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 (ISS) [Technology development]

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]

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] In Situ Sequencing (ISS) [Collaborative]

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]

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 (ISS) [Service]

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]

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]

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 Support for Computational Resources [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

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

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 Support for Computational Resources [Service]

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]

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]

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 Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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 Support for Computational Resources [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

J. Infect. Dis. 218 (3) 453-465 [2018-07-02; online 2017-12-23]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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

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]

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] Integrated Microscopy Technologies Stockholm [Collaborative]

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] Tissue Profiling

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] PLA and Single Cell Proteomics