Episode 50: Imaging pipelines and analysis, with Krešimir Beštak

In this milestone 50th episode of the Nextflow podcast, host Phil Ewels sits down with Krešimir Beštak, a PhD student and active contributor to the nf-core community, to explore an exciting frontier in bioinformatics: microscopy and spatial omics.

While Nextflow is traditionally associated with genomics workflows, Krešimir shares how it’s being used to power image analysis pipelines like MCMICRO, supporting complex research into cardiovascular disease and cancer diagnostics. Based at the University Hospital Heidelberg, Krešimir discusses his transition from master’s student to PhD researcher, the translational applications of spatial proteomics, and how Nextflow enables reproducible workflows far beyond its original scope.

00:00 Podcast Ep 50: Krešimir
00:09 Welcome and introductions
03:13 Introduction to Spatial Omics
04:26 Multiplexing markers
06:38 Metabolite microscopy
07:23 Myocardial multiomics
08:58 Microscopy data analysis
11:32 nf-core/mcmicro
13:05 2D vs 3D microscopy
13:38 Computational bottlenecks within analysis
15:43 Other nf-core imaging pipelines
18:36 Downstream analysis after molkart
19:53 Manual interventions
23:27 Minerva
25:39 Google Maps for cells
27:16 Microscopy community around Nextflow
30:34 How to get involved
31:38 Changes in Nextflow for microscopy
32:43 Nextflow Ambassador program
33:17 Conclusion