CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels. - Kimmo Kartasalo; Risto-Pekka Pölönen; Marisa Ojala; Jyrki Rasku; Jukka Lekkala; Katriina Aalto-Setälä; Pasi Kallio (BMC Bioinform., 2015)

Benchmarking of algorithms for 3D tissue reconstruction. - Kimmo Kartasalo; Leena Latonen; Tapio Visakorpi; Matti Nykter; Pekka Ruusuvuori (ICIP, 2016)

A software tool for studying the size and shape of human cardiomyocytes. - Jyrki Rasku; Marisa Ojala; Risto-Pekka Pölönen; Henry Joutsijoki; Yulia Gizatdinova; Jorma Laurikkala; Kimmo Kartasalo; Katriina Aalto-Setälä; Martti Juhola (Biomed. Signal Process. Control., 2016)

Dual Structured Convolutional Neural Network with Feature Augmentation for Quantitative Characterization of Tissue Histology. - Mira Valkonen; Kimmo Kartasalo; Kaisa Liimatainen; Matti Nykter; Leena Latonen; Pekka Ruusuvuori (ICCV Workshops, 2017)

Comparative analysis of tissue reconstruction algorithms for 3D histology. - Kimmo Kartasalo; Leena Latonen; Jorma Vihinen; Tapio Visakorpi; Matti Nykter; Pekka Ruusuvuori (Bioinform., 2018)

3D-Printed Whole Prostate Models with Tumor Hotspots Using Dual-Extruder Printer. - Kaisa Liimatainen; Leena Latonen; Kimmo Kartasalo; Pekka Ruusuvuori (EMBC, 2019)

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)

The importance of study design in the application of artificial intelligence methods in medicine. - Martin Eklund; Kimmo Kartasalo; Henrik Olsson; Peter Ström (npj Digit. Medicine, 2019)

Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration. - Kaisa Liimatainen; Leena Latonen; Masi Valkonen; Kimmo Kartasalo; Pekka Ruusuvuori (CoRR, 2020)

Detection of Perineural Invasion in Prostate Needle Biopsies with Deep Neural Networks. - Peter Ström; Kimmo Kartasalo; Pekka Ruusuvuori; Henrik Grönberg; Hemamali Samaratunga; Brett Delahunt; Toyonori Tsuzuki; Lars Egevad; Martin Eklund (CoRR, 2020)

Predicting molecular phenotypes from histopathology images: a transcriptome-wide expression-morphology analysis in breast cancer. - Yinxi Wang; Kimmo Kartasalo; Masi Valkonen; Christer Larsson; Pekka Ruusuvuori; Johan Hartman; Mattias Rantalainen (CoRR, 2020)

ANHIR: Automatic Non-Rigid Histological Image Registration Challenge. - Jirí Borovec; Jan Kybic; Ignacio Arganda-Carreras; Dmitry V. Sorokin; Gloria Bueno; Alexander V. Khvostikov; Spyridon Bakas; Eric I-Chao Chang; Stefan Heldmann; Kimmo Kartasalo; Leena Latonen; Johannes Lotz 002; et al. (IEEE Trans. Medical Imaging, 2020)

OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology. - Nita Mulliqi; Kimmo Kartasalo; Henrik Olsson; Xiaoyi Ji; Lars Egevad; Martin Eklund; Pekka Ruusuvuori (Bioinform., 2021)

Machine Learning and 3D Reconstruction Methods for Computational Pathology. - Kimmo Kartasalo (2021)

Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks. - Philippe Weitz; Yinxi Wang; Kimmo Kartasalo; Lars Egevad; Johan Lindberg; Henrik Grönberg; Martin Eklund; Mattias Rantalainen (Bioinform., 2022)

ACROBAT - a multi-stain breast cancer histological whole-slide-image data set from routine diagnostics for computational pathology. - Philippe Weitz; Masi Valkonen; Leslie Solorzano; Circe Carr; Kimmo Kartasalo; Constance Boissin; Sonja Koivukoski; Aino Kuusela; Dusan Rasic; Yanbo Feng; Sandra Kristiane Sinius Pouplier; Abhinav Sharma; et al. (CoRR, 2022)

Physical Color Calibration of Digital Pathology Scanners for Robust Artificial Intelligence Assisted Cancer Diagnosis. - Xiaoyi Ji; Richard Salmon; Nita Mulliqi; Umair Khan; Yinxi Wang; Anders Blilie; Henrik Olsson; Bodil Ginnerup Pedersen; Karina Dalsgaard Sørensen; Benedicte Parm Ulhøi; Svein Reidar Kjosavik; Emilius A. M. Janssen; et al. (CoRR, 2023)

RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy. - Øystein Øvrebø; Miina Ojansivu; Kimmo Kartasalo; Hanna M. G. Barriga; Petter Ranefall; Margaret N. Holme; Molly M. Stevens (BMC Bioinform., 2023)

The ACROBAT 2022 challenge: Automatic registration of breast cancer tissue. - Philippe Weitz; Masi Valkonen; Leslie Solorzano; Circe Carr; Kimmo Kartasalo; Constance Boissin; Sonja Koivukoski; Aino Kuusela; Dusan Rasic; Yanbo Feng; Sandra Kristiane Sinius Pouplier; Abhinav Sharma; et al. (Medical Image Anal., 2024)

Hierarchical Vision Transformers for prostate biopsy grading: Towards bridging the generalization gap. - Clément Grisi; Kimmo Kartasalo; Martin Eklund; Lars Egevad; Jeroen van der Laak; Geert Litjens 001 (Medical Image Anal., 2025)

Foundation Models - A Panacea for Artificial Intelligence in Pathology? - Nita Mulliqi; Anders Blilie; Xiaoyi Ji; Kelvin Szolnoky; Henrik Olsson; Sol Erika Boman; Matteo Titus; Geraldine Martinez Gonzalez; Julia Anna Mielcarz; Masi Valkonen; Einar Gudlaugsson; Svein Reidar Kjosavik; et al. (CoRR, 2025)

The impact of tissue detection on diagnostic artificial intelligence algorithms in digital pathology. - Sol Erika Boman; Nita Mulliqi; Anders Blilie; Xiaoyi Ji; Kelvin Szolnoky; Einar Gudlaugsson; Emiel A. M. Janssen; Svein Reidar Kjosavik; José Asenjo; Marcello Gambacorta; Paolo Libretti; Marcin Braun; et al. (CoRR, 2025)

Artificial Intelligence-Assisted Prostate Cancer Diagnosis for Reduced Use of Immunohistochemistry. - Anders Blilie; Nita Mulliqi; Xiaoyi Ji; Kelvin Szolnoky; Sol Erika Boman; Matteo Titus; Geraldine Martinez Gonzalez; José Asenjo; Marcello Gambacorta; Paolo Libretti; Einar Gudlaugsson; Svein Reidar Kjosavik; et al. (CoRR, 2025)