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

Informazioni relative al progetto

TissueMaps

ID dell’accordo di sovvenzione: 682810

DOI

10.3030/682810

Progetto chiuso

Data della firma CE 14 Marzo 2016

Data di avvio 1 Aprile 2016

Data di completamento 31 Marzo 2022

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 738 690,00

Contributo UE

€ 1 738 690,00

Coordinato da

UPPSALA UNIVERSITET
Sweden

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (13)

Machine learning for cell classification and neighborhood analysis in glioma tissue

Autori: Leslie Solorzano; Lina Wik; Thomas Olsson Bontell; Thomas Olsson Bontell; Yuyu Wang; Anna H. Klemm; Anna H. Klemm; Johan Öfverstedt; Asgeir Store Jakola; Asgeir Store Jakola; Arne Östman; Carolina Wählby; Carolina Wählby
Pubblicato in: Cytometry, Numero 4, 2021, ISSN 1552-4922
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/cyto.a.24467

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

Autori: Gabriele Partel, Markus M. Hilscher, Giorgia Milli, Leslie Solorzano, Anna H. Klemm, Mats Nilsson, Carolina Wählby
Pubblicato in: BMC Biology, Numero 18/1, 2020, ISSN 1741-7007
Editore: BioMed Central
DOI: 10.1186/s12915-020-00874-5

Spage2vec: Unsupervised representation of localized spatial gene expression signatures

Autori: Gabriele Partel, Carolina Wählby
Pubblicato in: The FEBS Journal, 2020, ISSN 1742-464X
Editore: Blackwell Publishing Inc.
DOI: 10.1111/febs.15572

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

Autori: Sajith Kecheril Sadanandan, Petter Ranefall, Sylvie Le Guyader, Carolina Wählby
Pubblicato in: Scientific Reports, Numero 7/1, 2017, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-017-07599-6

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

Autori: Damian J. Matuszewski, Anders Hast, Carolina Wählby, Ida-Maria Sintorn
Pubblicato in: PLOS ONE, Numero 12/11, 2017, Pagina/e e0188496, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0188496

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

Autori: 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
Pubblicato in: Nature Communications, Numero 8/1, 2017, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-017-01642-w

Deep Learning in Image Cytometry: A Review

Autori: 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
Pubblicato in: Cytometry Part A, Numero 95/4, 2019, Pagina/e 366-380, ISSN 1552-4922
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/cyto.a.23701

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

Autori: Leslie Solorzano, Gabriele Partel, Carolina Wählby
Pubblicato in: Bioinformatics, 2020, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa541

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

Autori: Hakan Wieslander, Philip J Harrison, Gabriel Skogberg, Sonya Jackson, Marcus Friden, Johan Karlsson, Ola Spjuth, Carolina Wahlby
Pubblicato in: IEEE Journal of Biomedical and Health Informatics, 2020, Pagina/e 1-1, ISSN 2168-2194
Editore: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/jbhi.2020.2996300

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

Autori: Nicolas Pielawski, Carolina Wählby
Pubblicato in: PLOS ONE, Numero 15/3, 2020, Pagina/e e0229839, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0229839

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

Autori: 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
Pubblicato in: The Lancet Oncology, Numero 21/2, 2020, Pagina/e 222-232, ISSN 1470-2045
Editore: The Lancet Publishing Group
DOI: 10.1016/s1470-2045(19)30738-7

14 th European congress on digital pathology

Autori: Leslie Solorzano, Carolina Wählby
Pubblicato in: Journal of Pathology Informatics, Numero 10/1, 2019, Pagina/e 32, ISSN 2153-3539
Editore: Association of Pathology Informatics
DOI: 10.4103/2153-3539.270744

Comparison of East-Asia and West-Europe cohorts explains disparities in survival outcomes and highlights predictive biomarkers of early gastric cancer aggressiveness.

Autori: Carla Pereira; Carla Pereira; Ji-Hyeon Park; Sofia Campelos; Irene Gullo; Carolina Lemos; Carolina Lemos; Leslie Solorzano; Diana Martins; Diana Martins; Diana Martins; Gilza Gonçalves; Dina Leitão; Hyuk-Joon Lee; Hyuk-Joon Lee; Seong-Ho Kong; Seong-Ho Kong; Ana André; Ana André; C. Borges; D. Almeida; Carolina Wälbhy; Raquel Almeida; Woo Ho Kim; Fátima Carneiro; Han-Kwang Yang; Han-Kwang Ya
Pubblicato in: International Journal of Cancer, Numero 7, 2021, ISSN 0020-7136
Editore: John Wiley & Sons Inc.
DOI: 10.1002/ijc.33872

Book chapters (1)

Decoding Gene Expression in 2D and 3D

Autori: Maxime Bombrun, Petter Ranefall, Joakim Lindblad, Amin Allalou, Gabriele Partel, Leslie Solorzano, Xiaoyan Qian, Mats Nilsson, Carolina Wählby
Pubblicato in: Lecture Notes in Computer Science (LNCS), Numero 10270, 2017, Pagina/e 257-268, ISBN 978-3-319-59128-5
Editore: Springer International Publishing
DOI: 10.1007/978-3-319-59129-2_22

Conference proceedings (2)

Whole Slide Image Registration for the Study of Tumor Heterogeneity

Autori: Leslie Solorzano, Gabriela M. Almeida, Bárbara Mesquita, Diana Martins, Carla Oliveira, Carolina Wählby
Pubblicato in: Computational Pathology and Ophthalmic Medical Image Analysis. OMIA 2018, COMPAY 2018. Lecture Notes in Computer Science, vol 11039. Springer, Cham, Numero vol 11039, 2018, Pagina/e 95-102, ISBN 978-3-030-00949-6
Editore: Springer International Publishing
DOI: 10.1007/978-3-030-00949-6_12

Transcriptome-Supervised Classification of Tissue Morphology Using Deep Learning

Autori: Axel Andersson, Gabriele Partel, Leslie Solorzano, Carolina Wahlby
Pubblicato in: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), 2020, Pagina/e 1630-1633, ISBN 978-1-5386-9330-8
Editore: IEEE
DOI: 10.1109/isbi45749.2020.9098361

Thesis and dissertations (1)

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

Autori: Giorgia Milli
Pubblicato in: 2018
Editore: Rel. Elisa Ficarra. Politecnico di Torino, Corso di laurea magistrale in Ingegneria Biomedica, 2018