Location: University of Helsinki main building (Fabianinkatu 33)
12:30 - 18:00 Registration
13:00 - 15:00 Workshops 1 (Recursion: Small Hall, 4th floor, ThinkCyte: F3017, 3rd floor)
Recursion: Biological Cartography: Building and Benchmarking Representations of Life
ThinkCyte: Ghost Cytometry: An AI-ML technology for High Resolution, Label-free Cellular Fingerprinting
15:00 - 15:30 Coffee Break
15:30 - 17:30 Workshops 2 (Small Hall, 4th floor)
Calico: Unbiased morphological profiling: state-of-the-art applications and emerging frontiers, including a panel discussion with panelists: Anne Carpenter, Juan Caicedo, Marta Fay, and Leena Latonen
17:30 - 18:00 Opening of the Symposium (Small Hall, 4th floor)
Welcome and practical matters by the Chairs Lassi Paavolainen and Pekka Ruusuvuori
CytoData Society by the President Juan Caicedo
18:00 - 19:00 Opening Keynote (Small Hall, 4th floor)
Berend Snijder, ETH Zurich: Image-based drug screening in human tissues for precision oncology
Location: University of Helsinki main building (Fabianinkatu 33)
08:30 - Registration open
09:00 - 10:30 Session 1: Spatial profiling (Small Hall, 4th floor)
09:00 - 09:45 Invited: Leeat Keren, Weizmann Institute of Science: Unraveling the tumor microenvironment by multiplexed imaging
09:45 - 10:00 Loan Vulliard, German Cancer Research Center: Integrating multiplexed imaging data with explainable panel-independent cellular profiling
10:00 - 10:15 Jovan Tanevski, Heidelberg University and Heidelberg University Hospital: Explainable models for global and local representation of spatial data
10:15 - 10:30 Juan C. Caicedo, Morgridge Institute for Research: CHAMMI: A benchmark for channel-adaptive models in microscopy imaging
10:30 - 11:00 Coffee Break
11:00 - 12:30 Session 2: Methods (Small Hall, 4th floor)
11:00 - 11:45 Invited: Wei Ouyang, KTH Royal Institute of Technology: Web and cloud infrastructure for AI-powered bioimage analysis
11:45 - 12:00 Kiran Saini, Deepcell, Inc.: Self-supervised Foundation Model Captures High-dimensional Morphology Data from Single Cell Brightfield Images
12:00 - 12:15 Mohammad Vali Sanian, Institute for Molecular Medicine Finland (FIMM): Decoupled Self-Supervised Training of Encoder-Decoder Transformers
12:15 - 12:30 Benjamin Morris, Allen Institute for Cell Science: CytoDL: a comprehensive deep-learning tool for streamlining microscopy image transformations
12:30 - 13:30 Lunch Break
13:30 - 15:00 Session 3: Cell Painting and Datasets (Small Hall, 4th floor)
13:30 - 14:15 Invited: Anne Carpenter, Broad Institute: Cell Painting: a decade of image-based profiling
14:15 - 14:30 Jesko Wagner, University of Edinburgh: Unlocking Single-Cell Morphological Profiling
14:30 - 14:45 Christopher Schmied, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin: Morphological profiling dataset based on the EU-OPENSCREEN bioactive library over two cell lines
14:45 - 15:00 Adam Taylor, Sage Bionetworks: Advancing FAIR data sharing for multiplexed tissue imaging data from the Human Tumor Atlas Network
15:00 - 15:30 Coffee Break
15:30 - 16:45 Session 4: Single-cell profiling (Small Hall, 4th floor)
15:30 - 16:15 Invited: Loïc A. Royer, Chan Zuckerberg Biohub: Self-supervised deep learning encodes high-resolution features of protein subcellular localization
16:15 - 16:30 Javed Iqbal, German Cancer Research Center: A global genetic interaction network by single-cell image analysis and machine learning
16:30 - 16:45 Nikita Moshkov, Biological Research Centre (BRC): Unbiased single-cell morphology with self-supervised vision transformers
16:45 - 18:00 Poster Session (Agora, 1st floor)
19:00 - 20:00 Reception hosted by the City of Helsinki (address: Pohjoisesplanadi 11-13)
Poster presentations:
#3 Emilia Piki, University of Oulu: ROR1-STAT3 signaling contributes to ovarian cancer intra-tumor heterogeneity
#4 Dominik Hirling, Biological Research Centre (BRC): Segmentation Metric Misinterpretations in Bioimage Analysis
#6 Veera Timonen, Institute for Molecular Medicine Finland (FIMM), University of Helsinki: Learning single-cell high-content phenotypes and their genetic determinants in healthy blood donors
#8 Irina Belaia, Turku BioImaging, Åbo Akademi University and University of Turku: Turku BioImaging image data services
#12 Benjamin Morris, Allen Institute for Cell Science: CytoDL: a comprehensive deep-learning tool for streamlining microscopy image transformations
#13 Joanna Pylvänäinen, Åbo Akademi University: Empowering insights into cancer metastasis: Advanced image analysis approaches for live cell imaging
#14 Dimitri Meistermann, University of Helsinki: Cell painting at single-cell level for characterization of Cortical Neuron Development in vitro
#15 Myriam Sevigny, University of Helsinki: Genome Biology Unit (GBU) - digital scanning at your service!
#16 Junel Solis, Turku BioImaging, Åbo Akademi University and University of Turku: Mouse Brain Alignment Tool: Software for autoradiography images
#17 Zsanett Zsófia Iván, Biological Research Centre: The proteomic map of mitosis
#18 Chun Hao Wong, Wellcome Sanger Institute: Optimising direct RNA in situ sequencing for optical pooled CRISPR screens
#19 Lakshmi Balasubramanian, Centre for Cellular and Molecular Platforms: A Constructive Approach of image-based profiling of single cells based on Image Flow Cytometry Data
#20 Fred Mast, Seattle Children's Research Institute: A graph convolutional neural network to decipher signal cascades controlling peroxisome biogenesis
#21 Javed Iqbal, German Cancer Research Center: A global genetic interaction network by single-cell image analysis and machine learning
#23 Martina K. Zowada, German Cancer Research Center (DKFZ): High-throughput AI-based phenotypic screening for drug discovery
#24 Zitong Chen, Broad Institute of MIT and Harvard: CHAMMI: A benchmark for channel-adaptive models in microscopy imaging
#26 Sonja Koivukoski, University of Eastern Finland: AI-driven Virtual Histological Staining
#27 Dado Tokic, Turku BioImaging, University of Turku & Åbo Akademi University: Collaboration between academia and industry in image analysis offers novel opportunities for both
#29 Christa Ringers, Uppsala University: Morphological profiling by Cell Painting to capture colorectal cancer disease heterogeneity
#30 Minttu Polso, Institute for Molecular Medicine Finland (FIMM), University of Helsinki: Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2
#33 Erik Serrano, University of Colorado Anschutz Medical Campus: CytoSnake: Orchestrating reproducible workflows with PyCytominer
#34 Isabel Mogollon, FIMM, University of Helsinki: AI-driven phenotypic image based interaction profiling for functional cancer precision medicine
#35 Antti Kiviaho, Tampere University and Tays Cancer Center: Image-based classification of uterine leiomyoma driver mutations using deep learning
#36 Taras Redchuk, University of Helsinki: Chromatin dynamics in serum starvation: machine learning-assisted analysis of tracking data
#37 Szymon Adamski, Ardigen: AI-driven identification of hits from Cell Painting based screening
#38 Ziqi Kang, Research Program in Systems Oncology, University of Helsinki: Tribus, a semi-automated cell-type classification tool for multiplexed imaging data
#39 Mari Tolonen, Novo Nordisk Center For Stem Cell Medicine (reNEW), University of Copenhagen: A workflow to observe single-cell morphogenetic features of developing mucociliary epidermis
#40 Yanthe Pearson, Center for Genomics and Systems Biology, New York University Abu Dhabi: A statistical framework for high-content phenotypic profiling using cellular feature distributions
#41 Fernando Perez, Research Program for Systems Oncology, University of Helsinki: A spatially resolved single-cell tumor microenvironment of clinicomolecular subtypes of high-grade serous ovarian cancer
#42 Ada Junquera, Research Program in Systems Oncology, University of Helsinki: Spatial landscape of cell cycle dynamics post-neoadjuvant chemotherapy in high-grade serous ovarian carcinoma
#43 Caroline Fandrey, Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn: Cell Type-Agnostic Optical Perturbation Screening Using In-Situ Sequencing
#44 Aleksandra Shabanova, Research Program in Systems Oncology, University of Helsinki: Assessing the importance of tumour microenvironment single-cell spatial features on clinicomolecular types of High-Grade Serous Ovarian Cancer with Machine Learning
Location: Biomedicum (Haartmaninkatu 8)
09:00 - 10:30 Introduction to the Hackathon
10:30 - 13:00 Hackathon
13:00 - 14:00 Lunch Break
14:00 - 18:00 Hackathon
18:00 - Social Event
Location: Biomedicum (Haartmaninkatu 8)
09:00 - 13:00 Hackathon
13:00 - 13:45 Lunch Break
13:45 - 15:30 Presentations, evaluations and announcing the winners!