Projects per year
Organization profile
Our research group focuses on uncovering complex information from bioimages using machine learning. We are interested in developing novel deep learning solutions for bioimage analysis, study various learning approaches to create general models, and to apply these methods and models to profile cancer cell and tissue samples imaged using fluorescence microscopy.
Fields of Science
- 113 Computer and information sciences
- 1182 Biochemistry, cell and molecular biology
International and National Collaboration
Publications and projects within past five years.
Profiles
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Gantugs Atarsaikhan
- Institute for Molecular Medicine Finland - Postdoctoral Researcher
Person: U2 Teaching and research staff
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Isabel Mogollon Figueroa
- Institute for Molecular Medicine Finland - Postdoctoral Researcher
- Bioimage Profiling
Person: U2 Teaching and research staff
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Lassi Paavolainen
- Institute for Molecular Medicine Finland - Academy Research Fellow
- Bioimage Profiling
- Doctoral Programme in Integrative Life Science - Supervisor for doctoral programme
Person: U3 Research and teaching staff
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Pan-cancer tumor microenvironment exploration with vision transformers
Paavolainen, L. & Mogollon Figueroa, I.
Syöpäsäätiö sr Cancerstiftelsen sr
01/01/2023 → 31/12/2023
Project: Foundations (Private Foundations, Non-Profit Foundations, Charitable Trusts)
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iCAN-DIP: AI-driven deep image-based profiling of pan-cancer tumor microenvironment
Atarsaikhan, G. & Paavolainen, L.
01/01/2023 → 31/12/2023
Project: Research project
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iCAN-DIP: AI-driven deep image-based profiling of pan-cancer tumor microenvironment
01/01/2023 → 31/12/2023
Project: Research project
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Uncovering patterns in cancer cells with visual representation learning
Paavolainen, L., Atarsaikhan, G. & Mogollon Figueroa, I.
01/09/2021 → 31/08/2026
Project: Research project
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Academy of Finland FIRI2020/ Biocenter Finland/ Single Cell Competence Center
Pietiäinen, V., Hassinen, A., Polso, M. M. M., Horvarth, P. & Paavolainen, L.
01/12/2020 → 31/12/2021
Project: Academy of Finland: Research infrastructure
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Fibroblast subsets in non-small cell lung cancer: Associations with survival, mutations, and immune features
Pellinen, T., Paavolainen, L., Martin-Bernabe, A., Araujo, R. P., Strell, C., Mezheyeuski, A., Backman, M., La Fleur, L., Brück, O., Sjolund, J., Holmberg, E., Välimäki, K., Brunnström, H., Botling, J., Moreno-Ruiz, P., Kallioniemi, O., Micke, P. & Östman, A., 10 Jan 2023, In: Journal of the National Cancer Institute. 115, 1, p. 71–82 12 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Foxi3 Suppresses Signaling Center Fate and is Necessary for the Early Development of Mouse Teeth
Mogollon Figueroa, I., 18 Jun 2022, In: bioRxiv. 46 p., 2022.07.18.500404.Research output: Contribution to journal › Article › Scientific
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Imaging Cellular Mechanisms of Oral Ectodermal Development and Disease
Mogollon Figueroa, I., 12 Sep 2022, University of Helsinki. 70 p.Research output: Thesis › Doctoral Thesis › Collection of Articles
Open Access -
Multiparametric platform for profiling lipid trafficking in human leukocytes
Pfisterer, S. G., Brock, I., Kanerva, K., Hlushchenko, I., Paavolainen, L., Ripatti, P., Islam, M. M., Kyttälä, A., Di Taranto, M. D., Scotto di Frega, A., Fortunato, G., Kuusisto, J., Horvath, P., Ripatti, S., Laakso, M. & Ikonen, E., 2022, In: Cell Reports Methods. 2, 2, 17 p., 100166.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Nucleus segmentation: towards automated solutions
Hollandi, R., Moshkov, N., Paavolainen, L., Tasnadi, E., Piccinini, F. & Horvath, P., Apr 2022, In: Trends in Cell Biology. 32, 4, p. 295-310 16 p.Research output: Contribution to journal › Review Article › peer-review
Open AccessFile
Activities
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Helsinki Institute of Life Science HiLIFE (Organisational unit)
Lassi Paavolainen (Chair)
1 Jan 2023 → …Activity: Membership types › Membership or other role in national/international committee, council, board
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3rd BioImage Informatics Finland symposium
Isabel Mogollon Figueroa (Attendee)
14 Nov 2022Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
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IEEE Transactions on Medical Imaging (Journal)
Lassi Paavolainen (Reviewer)
17 Oct 2022 → 4 Jan 2023Activity: Publication peer-review and editorial work types › Peer review of manuscripts
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Combining intra and inter cell feature representation
Gantugs Atarsaikhan (Speaker)
14 Nov 2022Activity: Talk or presentation types › Oral presentation
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SCANDEM 2022 - Nordic Microscopy Society Annual Meeting
Lassi Paavolainen (Attendee)
20 Jun 2022 → 22 Jun 2022Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars