Wählby C

Family name	Wählby
Given name	Carolina
Initials	C
ORCID	ORCID 0000-0002-4139-7003
Affiliations	Department of Information Technology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

32 publications

PubMed DOI Crossref

Rapid label-free identification of seven bacterial species using microfluidics, single-cell time-lapse phase-contrast microscopy, and deep learning-based image and video classification.

Hallström E, Kandavalli V, Wählby C, Hast A

PLoS ONE 20 (9) e0330265 [2025-09-08; online 2025-09-08]

DOI Crossref

Spatial mapping of proteins and their activity states in cancer models by multiplex in situ PLA

Löf L, Xu B, Sinha TK, ..., Zieba-Wicher A, Landegren U

- - (-) - [2025-07-11; online 2025-07-11]

PubMed DOI Crossref

CombiANT reader: Deep learning-based automatic image processing tool to robustly quantify antibiotic interactions.

Hallström E, Fatsis-Kavalopoulos N, Bimpis M, ..., Hast A, Andersson DI

PLOS Digit Health 4 (7) e0000669 [2025-07-00; online 2025-07-08]

PubMed DOI Crossref

Combining spatial transcriptomics with tissue morphology.

Chelebian E, Avenel C, Wählby C

Nat Commun 16 (1) 4452 [2025-05-13; online 2025-05-13]

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]

PubMed DOI Crossref

A clinical prostate biopsy dataset with undetected cancer.

Chelebian E, Avenel C, Järemo H, ..., Wählby C, Bergh A

Sci Data 12 (1) 423 [2025-03-11; online 2025-03-11]

DOI Crossref

Predicting allergy and postpartum depression from an incomplete compositional microbiome

Shternshis A, Tong B, Skalkidou A, ..., Hugerth LW, Singh P

- - (-) - [2025-03-06; online 2025-03-06]

DDLS Fellow Luisa Hugerth Prashant Singh SciLifeLab Fellow

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]

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]

DOI Crossref

Discovery of tumour indicating morphological changes in benign prostate biopsies through AI

Chelebian E, Avenel C, Järemo H, ..., Bergh A, Wählby C

- - (-) - [2024-06-19; online 2024-06-19]

PubMed DOI Crossref

PACMan: A software package for automated single-cell chlorophyll fluorometry.

Pontén O, Xiao L, Kutter J, ..., Wählby C, Behrendt L

Cytometry A 105 (3) 203-213 [2024-03-00; online 2023-10-20]

Lars Behrendt SciLifeLab Fellow

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]

DOI Crossref

Visualization & Quality Control Tools for Large-scale Multiplex Tissue Analysis in TissUUmaps 3

Behanova A, Avenel C, Andersson A, ..., Östman A, Wählby C

- - (-) - [2022-12-02; online 2022-12-02]

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]

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]

DOI Crossref

SimSearch: A Human-in-the-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images

Gupta A, Sabirsh A, Wählby C, Sintorn IM

- - (-) - [2022-04-07; online 2022-04-07]

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

- - (-) - [2022-01-28; online 2022-01-28]

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]

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 99 (12) 1176-1186 [2021-12-00; online 2021-06-22]

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]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Genes in human obesity loci are causal obesity genes in C. elegans.

Ke W, Reed JN, Yang C, ..., Civelek M, O'Rourke EJ

PLoS Genet 17 (9) e1009736 [2021-09-00; online 2021-09-07]

DOI Crossref

De novo spatiotemporal modelling of cell-type signatures identifies novel cell populations in the developmental human heart

Salas SM, Yuan X, Sylven C, ..., Wählby C, Partel G

- - (-) - [2021-07-11; online 2021-07-11]

PubMed DOI Crossref

Spage2vec: Unsupervised representation of localized spatial gene expression signatures.

Partel G, Wählby C

FEBS J. 288 (6) 1859-1870 [2021-03-00; online 2020-10-11]

DOI Crossref

Machine learning for cell classification and neighborhood analysis in glioma tissue

Solorzano L, Wik L, Bontell TO, ..., Östman A, Wählby C

- - (-) - [2021-02-27; online 2021-02-27]

PubMed DOI Crossref

TEM image restoration from fast image streams.

Wieslander H, Wählby C, Sintorn IM

PLoS ONE 16 (2) e0246336 [2021-02-01; online 2021-02-01]

DOI Crossref

Deep learning models for lipid-nanoparticle-based drug delivery

Harrison PJ, Wieslander H, Sabirsh A, ..., Wählby C, Spjuth O

- - (-) - [2020-04-07; online 2020-04-07]

PubMed DOI Crossref

Introducing Hann windows for reducing edge-effects in patch-based image segmentation.

Pielawski N, Wählby C

PLoS ONE 15 (3) e0229839 [2020-03-12; online 2020-03-12]

DOI Crossref

Spage2vec: Unsupervised detection of spatial gene expression constellations

Partel G, Wählby C

- - (-) - [2020-02-13; online 2020-02-13]

DOI Crossref

Identification of spatial compartments in tissue from in situ sequencing data

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

- - (-) - [2019-09-18; online 2019-09-18]

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]

DDLS Fellow Kimmo Kartasalo

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) 7860 [2017-08-10; online 2017-08-10]

PubMed DOI Crossref

The quest for multiplexed spatially resolved transcriptional profiling.

Wählby C

Nat. Methods 13 (8) 623-624 [2016-07-28; online 2016-07-29]