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Integrating spatial and genetic information via automated image analysis and interactive visualization of tissue data

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Automated identification of the mouse brain’s spatial compartments from in situ sequencing data

Author(s): Gabriele Partel, Markus M. Hilscher, Giorgia Milli, Leslie Solorzano, Anna H. Klemm, Mats Nilsson, Carolina Wählby
Published in: BMC Biology, Issue 18/1, 2020, ISSN 1741-7007
DOI: 10.1186/s12915-020-00874-5

Spage2vec: Unsupervised representation of localized spatial gene expression signatures

Author(s): Gabriele Partel, Carolina Wählby
Published in: The FEBS Journal, 2020, ISSN 1742-464X
DOI: 10.1111/febs.15572

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

Author(s): Sajith Kecheril Sadanandan, Petter Ranefall, Sylvie Le Guyader, Carolina Wählby
Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322
DOI: 10.1038/s41598-017-07599-6

A short feature vector for image matching: The Log-Polar Magnitude feature descriptor

Author(s): Damian J. Matuszewski, Anders Hast, Carolina Wählby, Ida-Maria Sintorn
Published in: PLOS ONE, Issue 12/11, 2017, Page(s) e0188496, ISSN 1932-6203
DOI: 10.1371/journal.pone.0188496

A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

Author(s): Jordi Carreras-Puigvert, Marinka Zitnik, Ann-Sofie Jemth, Megan Carter, Judith E. Unterlass, Björn Hallström, Olga Loseva, Zhir Karem, José Manuel Calderón-Montaño, Cecilia Lindskog, Per-Henrik Edqvist, Damian J. Matuszewski, Hammou Ait Blal, Ronnie P. A. Berntsson, Maria Häggblad, Ulf Martens, Matthew Studham, Bo Lundgren, Carolina Wählby, Erik L. L. Sonnhammer, Emma Lundberg, Pål Stenmar
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
DOI: 10.1038/s41467-017-01642-w

Deep Learning in Image Cytometry: A Review

Author(s): Anindya Gupta, Philip J. Harrison, Håkan Wieslander, Nicolas Pielawski, Kimmo Kartasalo, Gabriele Partel, Leslie Solorzano, Amit Suveer, Anna H. Klemm, Ola Spjuth, Ida‐Maria Sintorn, Carolina Wählby
Published in: Cytometry Part A, Issue 95/4, 2019, Page(s) 366-380, ISSN 1552-4922
DOI: 10.1002/cyto.a.23701

TissUUmaps: Interactive visualization of large-scale spatial gene expression and tissue morphology data

Author(s): Leslie Solorzano, Gabriele Partel, Carolina Wählby
Published in: Bioinformatics, 2020, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btaa541

Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images

Author(s): Hakan Wieslander, Philip J Harrison, Gabriel Skogberg, Sonya Jackson, Marcus Friden, Johan Karlsson, Ola Spjuth, Carolina Wahlby
Published in: IEEE Journal of Biomedical and Health Informatics, 2020, Page(s) 1-1, ISSN 2168-2194
DOI: 10.1109/jbhi.2020.2996300

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

Author(s): Nicolas Pielawski, Carolina Wählby
Published in: PLOS ONE, Issue 15/3, 2020, Page(s) e0229839, ISSN 1932-6203
DOI: 10.1371/journal.pone.0229839

Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study

Author(s): 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, Glen Kristiansen, Theodorus H van der Kwast, Katia R M Leite, Jesse K McKenney, Jon Oxley, Chin-Chen Pan, Hemamali Samaratunga, John R Srigley, Hiroyuki Takahashi, Toyonori Tsuzuki, Murali Varma, Mi
Published in: The Lancet Oncology, Issue 21/2, 2020, Page(s) 222-232, ISSN 1470-2045
DOI: 10.1016/s1470-2045(19)30738-7

14 th European congress on digital pathology

Author(s): Leslie Solorzano, Carolina Wählby
Published in: Journal of Pathology Informatics, Issue 10/1, 2019, Page(s) 32, ISSN 2153-3539
DOI: 10.4103/2153-3539.270744

Decoding Gene Expression in 2D and 3D

Author(s): Maxime Bombrun, Petter Ranefall, Joakim Lindblad, Amin Allalou, Gabriele Partel, Leslie Solorzano, Xiaoyan Qian, Mats Nilsson, Carolina Wählby
Published in: Lecture Notes in Computer Science (LNCS), Issue 10270, 2017, Page(s) 257-268
DOI: 10.1007/978-3-319-59129-2_22

Whole Slide Image Registration for the Study of Tumor Heterogeneity

Author(s): Leslie Solorzano, Gabriela M. Almeida, Bárbara Mesquita, Diana Martins, Carla Oliveira, Carolina Wählby
Published in: Computational Pathology and Ophthalmic Medical Image Analysis. OMIA 2018, COMPAY 2018. Lecture Notes in Computer Science, vol 11039. Springer, Cham, Issue vol 11039, 2018, Page(s) 95-102
DOI: 10.1007/978-3-030-00949-6_12

Transcriptome-Supervised Classification of Tissue Morphology Using Deep Learning

Author(s): Axel Andersson, Gabriele Partel, Leslie Solorzano, Carolina Wahlby
Published in: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), 2020, Page(s) 1630-1633
DOI: 10.1109/isbi45749.2020.9098361

Improving recall of In situ sequencing by self-learned features and classical image analysis techniques

Author(s): Giorgia Milli
Published in: 2018