Group leader, Principal Investigator, PhD

Peter Horvath is currently a group leader at FIMM as well as group leader and a director of Institute of Biochemistry at the Biological Research Center of the Hungarian Academia of Sciences in Szeged. He hold a Tekes/Business Finland Finnish Distinguished Professor (FiDiPro) Fellow position at FIMM 2014-2018. He graduated as a software engineer and mathematician, and received his Ph.D. from INRIA and University of Nice, Sophia Antipois, France in satellite image analysis. Between 2007 and 2013 he was a senior scientist at the ETH Zurich, in the Light Microscopy Centre.

Peter Horvath is interested in solving computational cell biology problems related to light microscopy and is involved in three main research fields; 2/3D biological image segmentation and tracking; development of microscopic image correction techniques and machine learning methods applied in high-throughput microscopy.

Postdoctoral Researcher, PhD

Lassi Paavolainen (Ph.D.) is an Academy of Finland Postdoctoral Fellow at the Institute for Molecular Medicine Finland (FIMM), University of Helsinki. He is currently working in project Deep learning for image-based profiling of cancer cells. In this project, his research focus is in deep convolutional neural networks (CNN's) and their applications to image analysis. He studies how CNN's can be utilized in segmentation of images and learning unbiased representation of microscopy images of cells from large collections of image data. The results of these studies are applied in cancer research.

Dr. Paavolainen obtained his PhD in 2013 from University of Jyväskylä, while working in Varpu Marjomäki's research group. During his PhD, he focused on image analysis method development for fluorescence microscopy and electron microscopy image data, and worked as the lead software engineer in open-source BioImageXD software project. Since 2015 he has worked at FIMM in Peter Horvath's research group. In close collaboration with Kallioniemi research group, he has focused on high-content image analysis of patient-derived cancer cells. In 2017, he co-created FIMM High-Content Imaging and Analysis core unit (FIMM-HCA) and worked as the first Head of the Unit.

In addition to research activities, currently, Dr. Paavolainen is President of the CytoData Society, representative of Finland in the management committee of COST project Network of European Bioimage Analysts NEUBIAS and Information Officer in the board of Nordic Microscopy Society.

 

Post-doctoral Researcher, Head of Unit, PhD

Antti Hassinen is the head of FIMM-HCA unit. He has previously worked in the Faculty of Biochemistry and Molecular Medicine in University of Oulu and gained his PhD in the group of Adj Prof Sakari Kellokumpu in 2013 working in the field of glycobiology and Golgi homeostasis in cancer cells. In the work he gained experience in molecular biology, cell biology, cytometry and microscopy techniques such as ratiometric pH measurements and image-based FRET as well as it’s applications in high throughput imaging.

His work in FIMM-HCA and the BIOMAG group is focused on providing open access high-throughput microscopy services to academic and commercial customers and collaborators and to apply in-house developed analysis tools into practice. One of the main research focuses is the development of 3D high-throughput microscopy and image analysis for use in drug sensitivity and resistance testing in close collaboration with the HTB FIMM unit.

Adjunct professor, PhD, Senior scientist

Vilja Pietiäinen is a senior scientist at the Institute for Molecular Medicine Finland (FIMM) and a team leader of personalized urological tumor project (DEDUCER) and ERAPerMed -funded project on clinical implementation of multidimensional phenotypical drug sensitivities in paediatric precision oncology (COMPASS).

Her research focuses on the systems medicine and precision therapeutics in cancer. She has M.Sc. in biochemistry and Ph.D. in virology/cell biology in 2005 (University of Edinburgh, U.K.; University of Helsinki-UH, Finland), and . Currently, she is particularly dedicated to develop high-content phenotypic image-based characterization and ex vivo drug testing of patient-derived cancer cell models.

Laboratory Coordinator, MSc

Involved in various single-cell related shenanigans. Recent focus in single-cell transcriptomics and morphology based cell recognition/isolation; utilizing high-content screening microscopy, image analysis, machine learning and laser microdissection microscopy.