Exploring subjective image quality through isopreference curves. - Antti Lehmussola; Pekka Ruusuvuori; Olli Yli-Harja (ICIP (1), 2005)

Three-Dimensional Digital Image Analysis of Immunostained Neurons in Thick Tissue Sections. - Jyrki Selinummi; Pekka Ruusuvuori; Antti Lehmussola; Heikki Huttunen; Olli Yli-Harja; Riitta Miettinen (EMBC, 2006)

Learning-based method for spot addressing in microarray images. - Pekka Ruusuvuori; Antti Lehmussola; Olli Yli-Harja (Image Processing: Algorithms and Systems, 2006)

Evaluating the performance of microarray segmentation algorithms. - Antti Lehmussola; Pekka Ruusuvuori; Olli Yli-Harja (Bioinform., 2006)

Simulation of microarray data with realistic characteristics. - Matti Nykter; Tommi Aho; Miika Ahdesmäki; Pekka Ruusuvuori; Antti Lehmussola; Olli Yli-Harja (BMC Bioinform., 2006)

Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells. - Antti Niemistö; Matti Nykter; Tommi Aho; Henna Jalovaara; Kalle Marjanen; Miika Ahdesmäki; Pekka Ruusuvuori; Mikko Tiainen; Marja-Leena Linne; Olli Yli-Harja (EURASIP J. Bioinform. Syst. Biol., 2007)

Computational Framework for Simulating Fluorescence Microscope Images With Cell Populations. - Antti Lehmussola; Pekka Ruusuvuori; Jyrki Selinummi; Heikki Huttunen; Olli Yli-Harja (IEEE Trans. Medical Imaging, 2007)

Benchmark set of synthetic images for validating cell image analysis algorithms. - Pekka Ruusuvuori; Antti Lehmussola; Jyrki Selinummi; Tiina Rajala; Heikki Huttunen; Olli Yli-Harja (EUSIPCO, 2008)

Object detection for dynamic adaptation of interconnections in inkjet printed electronics. - Heikki Huttunen; Pekka Ruusuvuori; Tapio Manninen; Kalle Rutanen; Risto Rönkkä; Ari Visa (ICIP, 2008)

Efficient automated method for image-based classification of microbial cells. - Pekka Ruusuvuori; Jenni Seppälä; Timo Erkkilä; Antti Lehmussola; Jaakko A. Puhakka; Olli Yli-Harja (ICPR, 2008)

Synthetic Images of High-Throughput Microscopy for Validation of Image Analysis Methods. - Antti Lehmussola; Pekka Ruusuvuori; Jyrki Selinummi; Tiina Rajala; Olli Yli-Harja (Proc. IEEE, 2008)

Identity verification based on vessel matching from fundus images. - Hannu Oinonen; Heikki Forsvik; Pekka Ruusuvuori; Olli Yli-Harja; Ville Voipio; Heikki Huttunen (ICIP, 2010)

Probabilistic analysis of gene expression measurements from heterogeneous tissues. - Timo Erkkilä; Saara Lehmusvaara; Pekka Ruusuvuori; Tapio Visakorpi; Ilya Shmulevich; Harri Lähdesmäki (Bioinform., 2010)

Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. - Pekka Ruusuvuori; Tarmo Äijö; Sharif Chowdhury; Cecilia Garmendia-Torres; Jyrki Selinummi; Mirko Birbaumer; Aimée M. Dudley; Lucas Pelkmans; Olli Yli-Harja (BMC Bioinform., 2010)

Polynomial pulp fiber modeling. - Heikki Huttunen; Hannu Oinonen; Jyrki Selinummi; Pekka Ruusuvuori; Ville Voipio (EUSIPCO, 2012)

Image segmentation using sparse logistic regression with spatial prior. - Pekka Ruusuvuori; Tapio Manninen; Heikki Huttunen (EUSIPCO, 2012)

Application independent greedy particle tracking method for 3D fluorescence microscopy image series. - Lassi Paavolainen; Pasi Kankaanpää; Pekka Ruusuvuori; Gregory McNerney; Mikko Karjalainen; Varpu Marjomaki (ISBI, 2012)

The eighth annual MLSP competition: Second place team. - Heikki Huttunen; Timo Erkkilä; Pekka Ruusuvuori; Tapio Manninen (MLSP, 2012)

Graph cut and image intensity-based splitting improves nuclei segmentation in high-content screening. - Muhammad Farhan; Pekka Ruusuvuori; Mario Emmenlauer; Pauli Rämö; Olli Yli-Harja; Christoph Dehio (Image Processing: Algorithms and Systems, 2013)

The 9th annual MLSP competition: New methods for acoustic classification of multiple simultaneous bird species in a noisy environment. - Forrest Briggs; Yonghong Huang; Raviv Raich; Konstantinos Eftaxias; Zhong Lei; William Cukierski; Sarah Frey Hadley; Adam Hadley; Matthew Betts; Xiaoli Z. Fern; Jed Irvine; Lawrence Neal; et al. (MLSP, 2013)

Multi-scale Gaussian representation and outline-learning based cell image segmentation. - Muhammad Farhan; Pekka Ruusuvuori; Mario Emmenlauer; Pauli Rämö; Christoph Dehio; Olli Yli-Harja (BMC Bioinform., 2013)

Training based cell detection from bright-field microscope images. - Tuomas Tikkanen; Pekka Ruusuvuori; Leena Latonen; Heikki Huttunen (ISPA, 2015)

Data-Driven Approach to Benthic Cover Type Classification Using Bathymetric LiDAR Waveform Analysis. - Teemu Kumpumäki; Pekka Ruusuvuori; Ville Kangasniemi; Tarmo Lipping (Remote. Sens., 2015)

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

Supervised method for cell counting from bright field focus stacks. - Kaisa Liimatainen; Pekka Ruusuvuori; Leena Latonen; Heikki Huttunen (ISBI, 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)

Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks. - Kaisa Liimatainen; Lauri Kananen; Leena Latonen; Pekka Ruusuvuori (BMC Bioinform., 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)

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)

Cytokeratin-Supervised Deep Learning for Automatic Recognition of Epithelial Cells in Breast Cancers Stained for ER, PR, and Ki-67. - Mira Valkonen; Jorma Isola; Onni Ylinen; Ville Muhonen; Anna Saxlin; Teemu Tolonen; Matti Nykter; Pekka Ruusuvuori (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)

Generalized Fixation Invariant Nuclei Detection Through Domain Adaptation Based Deep Learning. - Mira Valkonen; Gunilla Högnäs; G. Steven Bova; Pekka Ruusuvuori (IEEE J. Biomed. Health Informatics, 2021)

Deformation equivariant cross-modality image synthesis with paired non-aligned training data. - Joel Honkamaa; Umair Khan; Sonja Koivukoski; Leena Latonen; Pekka Ruusuvuori; Pekka Marttinen (CoRR, 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)

Domain-specific transfer learning in the automated scoring of tumor-stroma ratio from histopathological images of colorectal cancer. - Liisa Petäinen; Juha P. Väyrynen; Pekka Ruusuvuori; Ilkka Pölönen; Sami Äyrämö; Teijo Kuopio (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)

Improving Performance in Colorectal Cancer Histology Decomposition using Deep and Ensemble Machine Learning. - Fabi Prezja; Leevi Annala; Sampsa Kiiskinen; Suvi Lahtinen; Timo Ojala; Pekka Ruusuvuori; Teijo Kuopio (CoRR, 2023)

The effect of neural network architecture on virtual H&E staining: Systematic assessment of histological feasibility. - Umair Khan; Sonja Koivukoski; Mira Valkonen; Leena Latonen; Pekka Ruusuvuori (Patterns, 2023)

Deformation equivariant cross-modality image synthesis with paired non-aligned training data. - Joel Honkamaa; Umair Khan; Sonja Koivukoski; Mira Valkonen; Leena Latonen; Pekka Ruusuvuori; Pekka Marttinen (Medical Image Anal., 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)

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)

Staining normalization in histopathology: Method benchmarking using multicenter dataset. - Umair Khan; Jouni Härkönen; Marjukka Friman; Leena Latonen; Teijo Kuopio; Pekka Ruusuvuori (CoRR, 2025)