Ruusuvuori lab
Pekka gave a talk at the 38th European Society of Pathology Congress in Stockholm on virtual staining as an alternative to H&E for diagnostic pathology. The talk was part of the session “AI in pathology: from automation to clinical decision support”, chaired by Johan Hartman and Eugenia Aleman Colón.
Nisar’s poster placed 2nd out of 108 entries at the 35th BioCity Symposium in Turku, where he presented work on AI driven bioimage analysis and histopathology under the SYS-Life programme. He also co-chaired the session “Cell Dynamics, Mechanobiology and Disease Mechanisms”.
At the 30th anniversary Medical Image Understanding and Analysis conference in Dublin, Pekka presented a new paper by Hesam Hakimnejad, Sonja Koivukoski, Leena Latonen and Pekka: “Residual Shifting-Based Diffusion Models for Virtual H&E Staining”. The method offers a more computationally efficient way to generate virtual H&E stains from unstained tissue.
Kaisa Liimatainen, Leena Latonen and Pekka published “SparStVR, exploring sparse 3D histology data in virtual reality” in Communications Engineering. The VR application lets you interactively explore 3D histology data with multimodal heatmap support.
Umair Khan, Jouni Härkönen, Marjukka Friman, Hesam Hakimnejad, Leena Latonen, Teijo Kuopio and Pekka published a multicenter benchmarking study on staining normalization in histopathology in Scientific Reports. The paper compares traditional and generative AI normalization methods and tests how robust foundation models are to staining variation.
Hyder Abbas, Sonja Koivukoski, Hesam Hakimnejad, Zsombor Malatinszki, Tuomas Mäkilä, Leena Latonen and Pekka won the Best Paper Award at the 6th IEEE Conference on ICT Solutions for eHealth in Vilamoura, Portugal, for “Transfer Learning Based on Generative Adversarial Network for Tissue-Specific Virtual Staining”. The group also presented a second paper at the conference, “StainFlow: Virtual Staining of Label-Free Tissue via Flow-Based Generative Models”, by Hesam Hakimnejad, Sonja Koivukoski, Leena Latonen and Pekka.
Hesam Hakimnejad, Hanga Tárkányi and Niloufar Rahimizadeh Asli represented the group at the 22nd European Congress on Digital Pathology in Graz, Austria, presenting our virtual staining research. Our collaborator Leena Latonen from the University of Eastern Finland gave an invited talk, and travel was supported by the InFLAMES Research Flagship.
ComPatAI, led by Pekka together with co-PIs Leena Latonen from the University of Eastern Finland and Artturi Mäkinen from Fimlab and Tampere University Hospital, was awarded computing resources in the 7th Finnish LUMI Extreme Scale Call. The consortium is building a foundation model for computational pathology using up to 1 million whole-slide images from Finnish university hospitals.
Pekka co-authored a new AI model for predicting DNA mismatch repair (dMMR) status in colorectal cancer from histopathology, published in Computer Methods and Programs in Biomedicine. Led by Liisa Petäinen and Jussi Väyrynen, the model uses non-tumor and low-magnification tissue regions to cut analysis time from days to minutes, and was validated across cohorts from Finland and the US.
Our collaborator Sonja Koivukoski from the University of Eastern Finland defended her PhD thesis, “Applicability of virtual staining in histological whole slide images”. Prof. Johanna Arola acted as opponent, with Leena Latonen as custos and Pekka as second supervisor. Congratulations, Sonja!