Programme

CytoData2023, October 23-26, includes the Symposium (workshops, presentations, and a poster session) and the Hackathon. The Symposium is scheduled for the first two days whereas the Hackathon happens during the last two days of the CytoData2023. The schedule can be seen below.
Monday, 23 October 2023

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

Tuesday, 24 October 2023

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

Wednesday, 25 October 2023

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

Thursday, 26 October 2023

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!