Hi everyone, to get things started I wanted to introduce myself: I’m at Janelia Research Campus, and I’ve been working together with @Cristian Goina on large scale image reconstruction and analysis, often with custom microscopes or protocols that are being designed here at Janelia. We have developed two image analysis pipelines in Nextflow so far: • https://github.com/JaneliaSciComp/multifish, for spatial transcriptomics using the EASI-FISH protocol. It takes raw microscopy imagery (CZI format) and produces a transcription profile for each cell. • https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction, for reconstructing neural circuits imaged with lattice lightsheet microscopy I presented the first one at the Nextflow Summit last year, which you can . We’re now starting to take parts of the multifish pipeline above and turn it into a general nf-core pipeline for lightsheet image reconstruction: • https://github.com/krokicki/nf-lightsheetrecon Very interested in what other folks are doing at the intersection of nf-core and microscopy 😁