PaintSHOP is a web-based platform for designing fluorescence in situ hybridization (FISH) experiments using oligonucleotide probes. It supports interactive design at both transcriptome and genome scales, bringing tools and resources for probe development together in one place. Users can launch PaintSHOP to design probes, consult the user guide for assistance, and explore existing collections of genome-wide DNA and RNA FISH probes. The site also provides sequence files that can be viewed and downloaded for use with those collections.

For researchers who need to create probe collections for a particular genome assembly, PaintSHOP offers a pipeline for generating them de novo. The pipeline uses Snakemake, a workflow-management system, to support the generation process. Together, the interactive design application, downloadable resources, and pipeline serve different stages of FISH probe work, from exploring available collections to building new ones. PaintSHOP also directs visitors to its associated research paper. The platform is presented by the Beliveau Lab and is intended to help users work with transcriptome- and genome-scale oligonucleotide FISH experiments.