Cell Detection by Functional Inverse Diffusion and Nonnegative Group Sparsity
On August 28, 2018, a Stockholm-based biotech company launched a new product: The Mabtech IRISTM, a next-generation FluoroSpot and ELISpot reader. The reader is a machine designed to analyze a type of biomedical image-based assays that are commonly used in immunology to study cell responses. The heart of this machine is an inverse problem and an algorithm that we developed at KTH in 2015.
The presentation will outline the problem of analyzing FluoroSpot assays from a signal processing perspective and explain the methods we designed to solve it. The problem essentially amounts to counting, localizing and quantifying heterogeneous diffuse spots in an image. The solution involves components such as the development of a tractable linear model from the physical properties that govern the reaction-diffusion-adsorption-desorption process in the assay; the formulation of an inverse problem in function spaces and its discretized approximation; the role of group sparsity in finding a plausible solution to an otherwise ill-posed problem; and how to efficiently solve the resulting 40 million variable optimization problem on a GPU.
Time: Fri 2019-04-05 11.00 - 12.00
Participating: Joakim Jaldén
Joakim Jaldén received the M.Sc. and Ph.D. in electrical engineering from the KTH Royal Institute of Technology, Stockholm, Sweden in 2002 and 2007 respectively. From July 2007 to June 2009 he held a post-doctoral research position at the Vienna University of Technology, Vienna, Austria. He also studied at Stanford University, CA, USA, from September 2000 to May 2002, and worked at ETH, Zürich, Switzerland, as a visiting researcher, from August to September, 2008. In July 2009, he returned to KTH, where he is now a Professor of Signal Processing. He was an associate editor for the IEEE Communications Letters between 2009 and 2011, and an associate editor for the IEEE Transactions in Signal Processing between 2012 and 2016. He has been a member of the IEEE Signal Processing for Communications and Networking Technical Committee (SPCOM-TC) since 2013 and will be the chair of the committee starting 2019. Since 2016 he is also responsible for the five-year Degree Program in Electrical Engineering (CELTE) at KTH.
For his work on MIMO communications, Joakim has been awarded the IEEE Signal Processing Society’s 2006 Young Author Best Paper Award, the Distinguished Achievement Award of NEWCOM++ Network of Excellence in Telecommunications 2007–2011, and the best student conference paper award at IEEE ICASSP 2007. He is also a recipient of the Ingvar Carlsson Career Award issued in 2009 by the Swedish Foundation for Strategic Research. His later interests include signal processing for biomedical data analysis. Earlier work in this field was awarded a conference best paper award at IEEE ISBI 2012, and subsequent work by the group has been awarded several Bitplane Awards in connection to the ISBI cell tracking challenges between 2013 and 2015. Later work on the analysis of FluoroSpot and ELISpot assays just saw its first commercial implementation.