Segmentation of Cell Nuclei in Tissue by Combining Seeded Watersheds with Gradient Information. - Carolina Wählby; Ewert Bengtsson (SCIA, 2003)

Algorithms for Applied Digital Image Cytometry. - Carolina Wählby (2003)

Easy-to-Use Object Selection by Color Space Projections and Watershed Segmentation. - Per Holting; Carolina Wählby (ICIAP, 2005)

Seeded Watersheds for Combined Segmentation and Tracking of Cells. - Amalka Pinidiyaarachchi; Carolina Wählby (ICIAP, 2005)

Time-Lapse Microscopy and Classification of in Vitro Cell Migration Using Hidden Markov Modeling. - Karin Althoff; Johan Degerman; Carolina Wählby; Thorleif Thorlin; Jonas Faijerson; Peter S. Eriksson; Tomas Gustavsson (ICASSP (5), 2006)

Finding Cells, finding moleculaes, finding patterns. - Carolina Wählby; Patrick Karlsson; Sara Henriksson; Chatarina Larsson; Mats F. Nilsson; Ewert Bengtsson (ICDM (Workshops), 2006)

Finding Cells, Finding Molecules, Finding Patterns. - Carolina Wählby; Patrick Karlsson; Sara Henriksson; Chatarina Larsson; Mats F. Nilsson; Ewert Bengtsson (MDA, 2007)

Image Based Measurements of Single Cell mtDNA Mutation Load. - Amin Allalou; Frans M. van de Rijke; Roos Jahangir Tafrechi; Anton K. Raap; Carolina Wählby (SCIA, 2007)

BlobFinder, a tool for fluorescence microscopy image cytometry. - Amin Allalou; Carolina Wählby (Comput. Methods Programs Biomed., 2009)

Resolving clustered worms via probabilistic shape models. - Carolina Wählby; Tammy Riklin-Raviv; Vebjorn Ljosa; Annie L. Conery; Polina Golland; Frederick M. Ausubel; Anne E. Carpenter (ISBI, 2010)

Morphology-Guided Graph Search for Untangling Objects: C. elegans Analysis. - Tammy Riklin Raviv; Vebjorn Ljosa; Annie L. Conery; Frederick M. Ausubel; Anne E. Carpenter; Polina Golland; Carolina Wählby (MICCAI (3), 2010)

Automated quantification of Zebrafish tail deformation for high-throughput drug screening. - Omer Ishaq; Joseph Negri; Mark-Anthony Bray; Alexandra Pacureanu; Randall T. Peterson; Carolina Wählby (ISBI, 2013)

Blind Color Decomposition of Histological Images. - Milan Gavrilovic; Jimmy C. Azar; Joakim Lindblad; Carolina Wählby; Ewert Bengtsson; Christer Busch; Ingrid B. Carlbom (IEEE Trans. Medical Imaging, 2013)

An Evaluation of the Faster STORM Method for Super-resolution Microscopy. - Omer Ishaq; Johan Elf; Carolina Wählby (ICPR, 2014)

Image based in situ sequencing for RNA analysis in tissue. - Alexandra Pacureanu; Rongqin Ke; Marco Mignardi; Mats F. Nilsson; Carolina Wählby (ISBI, 2014)

Feature Augmented Deep Neural Networks for Segmentation of Cells. - Sajith Kecheril Sadanandan; Petter Ranefall; Carolina Wählby (ECCV Workshops (1), 2016)

Comparison of Flow Cytometry and Image-Based Screening for Cell Cycle Analysis. - Damian J. Matuszewski; Ida-Maria Sintorn; Jordi Carreras Puigvert; Carolina Wählby (ICIAR, 2016)

Fast adaptive local thresholding based on ellipse fit. - Petter Ranefall; Sajith Kecheril Sadanandan; Carolina Wählby (ISBI, 2016)

Segmentation and Track-Analysis in Time-Lapse Imaging of Bacteria. - Sajith Kecheril Sadanandan; Ozden Baltekin; Klas E. G. Magnusson; Alexis Boucharin; Petter Ranefall; Joakim Jaldén; Johan Elf; Carolina Wählby (IEEE J. Sel. Top. Signal Process., 2016)

Deep Convolutional Neural Networks for Detecting Cellular Changes Due to Malignancy. - Gustav Forslid; Håkan Wieslander; Ewert Bengtsson; Carolina Wählby; Jan-Michael Hirsch; Christina Runow Stark; Sajith Kecheril Sadanandan (ICCV Workshops, 2017)

Spheroid Segmentation Using Multiscale Deep Adversarial Networks. - Sajith Kecheril Sadanandan; Johan Karlsson; Carolina Wählby (ICCV Workshops, 2017)

Decoding Gene Expression in 2D and 3D. - Maxime Bombrun; Petter Ranefall; Joakim Lindblad; Amin Allalou; Gabriele Partel; Leslie Solorzano; Xiaoyan Qian; Mats F. Nilsson; Carolina Wählby (SCIA (2), 2017)

Bridging Histology and Bioinformatics - Computational Analysis of Spatially Resolved Transcriptomics. - Marco Mignardi; Omer Ishaq; Xiaoyan Qian; Carolina Wählby (Proc. IEEE, 2017)

Whole Slide Image Registration for the Study of Tumor Heterogeneity. - Leslie Solorzano; Gabriela M. Almeida; Bárbara Mesquita; Diana Martins; Carla Oliveira; Carolina Wählby (COMPAY/OMIA@MICCAI, 2018)

Improving Recall of In Situ Sequencing by Self-Learned Features and a Graphical Model. - Gabriele Partel; Giorgia Milli; Carolina Wählby (CoRR, 2018)

Pathologist-Level Grading of Prostate Biopsies with Artificial Intelligence. - Peter Ström; Kimmo Kartasalo; Henrik Olsson; Leslie Solorzano; Brett Delahunt; Daniel M. Berney; David G. Bostwick; Andrew J. Evans; David J. Grignon; Peter A. Humphrey; Kenneth A. Iczkowski; James G. Kench; et al. (CoRR, 2019)

Introducing Hann windows for reducing edge-effects in patch-based image segmentation. - Nicolas Pielawski; Carolina Wählby (CoRR, 2019)

Graph-based image decoding for multiplexed in situ RNA detection. - Gabriele Partel; Carolina Wählby (ICPR, 2020)

Transcriptome-Supervised Classification of Tissue Morphology Using Deep Learning. - Axel Andersson; Gabriele Partel; Leslie Solorzano; Carolina Wählby (ISBI, 2020)

Weakly-Supervised Prediction of Cell Migration Modes in Confocal Microscopy Images Using Bayesian Deep Learning. - Anindya Gupta; Veronica Larsson; Damian J. Matuszewski; Staffan Strömblad; Carolina Wählby (ISBI, 2020)

In Silico Prediction of Cell Traction Forces. - Nicolas Pielawski; Jianjiang Hu; Staffan Strömblad; Carolina Wählby (ISBI, 2020)

CoMIR: Contrastive Multimodal Image Representation for Registration. - Nicolas Pielawski; Elisabeth Wetzer; Johan Öfverstedt; Jiahao Lu; Carolina Wählby; Joakim Lindblad; Natasa Sladoje (NeurIPS, 2020)

TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data. - Leslie Solorzano; Gabriele Partel; Carolina Wählby (Bioinform., 2020)

Towards Automatic Protein Co-Expression Quantification in Immunohistochemical TMA Slides. - Leslie Solorzano; Carla Pereira 005; Diana Martins; Raquel Almeida 003; Fátima Carneiro; Gabriela M. Almeida; Carla Oliveira; Carolina Wählby (IEEE J. Biomed. Health Informatics, 2021)

Deep Learning With Conformal Prediction for Hierarchical Analysis of Large-Scale Whole-Slide Tissue Images. - Håkan Wieslander; Philip J. Harrison; Gabriel Skogberg; Sonya Jackson; Hakan Fridén; Johan Karlsson; Ola Spjuth; Carolina Wählby (IEEE J. Biomed. Health Informatics, 2021)

Label-free Estimation of Sarcomere Orientation from Brightfield Microscopy Images of Induced Pluripotent Stem Cell Derived Cardiomyocyte Nuclei. - Antti Ahola; Birhanu Belay; Carolina Wählby; Jari A. K. Hyttinen (CinC, 2022)

Seeded iterative clustering for histology region identification. - Eduard Chelebian; Francesco Ciompi; Carolina Wählby (CoRR, 2022)

De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks. - Sergio Marco Salas; Xiao Yuan 005; Christer Sylven; Mats F. Nilsson; Carolina Wählby; Gabriele Partel (PLoS Comput. Biol., 2022)

SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images. - Ankit Gupta 018; Alan Sabirsh; Carolina Wählby; Ida-Maria Sintorn (IEEE J. Biomed. Health Informatics, 2022)

Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning. - Axel Andersson; Andrea Behanova; Carolina Wählby; Filip Malmberg (GbRPR, 2023)

Evaluating the utility of brightfield image data for mechanism of action prediction. - Philip J. Harrison; Ankit Gupta 018; Jonne Rietdijk; Håkan Wieslander; Jordi Carreras Puigvert; Polina Georgiev; Carolina Wählby; Ola Spjuth; Ida-Maria Sintorn (PLoS Comput. Biol., 2023)

Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy. - Erik Hallström; Vinodh Kandavalli; Petter Ranefall; Johan Elf; Carolina Wählby (PLoS Comput. Biol., 2023)

Self-Supervised Learning for Genetically Relevant Domain Identification in Morphological Images. - Eduard Chelebian; Christophe Avenel; Carolina Wählby (ISBI, 2024)

Learned morphological features guide cell type assignment of deconvolved spatial transcriptomics. - Eduard Chelebian; Christophe Avenel; Julio León; Chung-Chau Hon; Carolina Wählby (MIDL, 2024)

What makes for good morphology representations for spatial omics? - Eduard Chelebian; Christophe Avenel; Carolina Wählby (CoRR, 2024)

DEPICTER: Deep representation clustering for histology annotation. - Eduard Chelebian; Christophe Avenel; Francesco Ciompi; Carolina Wählby (Comput. Biol. Medicine, 2024)

Segmentation-free integration of nuclei morphology and spatial transcriptomics for retinal images. - Eduard Chelebian; Pratiti Dasgupta; Zainalabedin Samadi; Carolina Wählby; Amjad Askary (CoRR, 2025)