HADES Exp35 dataset: Potato root colonisation dynamics by Pseudomonas simiae WCS417 and Pseudomonas capeferrum WCS358 across host genotypes

HADES Exp35 is a longitudinal potato root-imaging dataset generated using the HADES automated phenotyping platform to examine bacterial root-colonisation dynamics across host and microbial genotypes. The experiment comprises the diploid hybrid true potato seed genotypes HYB007 and RP043 under mock treatment or inoculation with mCherry-labelled Pseudomonas simiae WCS417 or Pseudomonas capeferrum WCS358. The methods study used the complete Exp35 experimental scope to compare genotype- and bacterial-strain-dependent colonisation patterns. True potato seeds were pre-germinated, and one-week-old seedlings were transplanted individually to plates containing ½ Murashige and Skoog medium without sucrose, solidified with 0.8% Gelrite. Plants were cultivated under controlled long-day conditions. Bacterial treatments were applied at the root-shoot junction using mCherry-labelled WCS417 or WCS358, with mock-treated plants serving as controls. In the experiment reported in the methods study, bacterial suspensions were applied as 10-µL droplets at OD₆₀₀ = 0.1. Plants were monitored using HADES RootCam transmitted-light and fluorescence imaging. Transmitted-light acquisitions provide longitudinal morphological records of potato root development, while mCherry fluorescence acquisitions provide imaging records associated with bacterial colonisation. The two fluorescent bacterial strains enable comparison of colonisation by WCS417 and WCS358 across the two potato genotypes. Longitudinal fluorescence imaging was used in the companion methods study to resolve both host-genotype- and bacterial-strain-dependent colonisation behaviour. Fluorescent WCS417 and WCS358 derivatives used for these assays carried the mCherry reporter, and bacterial fluorescence was acquired using the RootCam fluorescence configuration. The public dataset preserves the acquisition and vendor-analysis record of the complete Exp35 experiment. It contains RootCam transmitted-light and fluorescence acquisition records together with corresponding PlantScreen Data Analyzer outputs where generated. The release additionally provides reviewed experimental metadata, package-scoped variable definitions, manifests, checksums, provenance mappings, and validation information. PlantScreen analysis products are retained as vendor-generated components of the exported experiment and should not be confused with the custom HADES segmentation and fluorescence-analysis products used for the biological analyses in the companion methods study. The HADES Data Descriptor release intentionally excludes the complete downstream segmentation, fluorescence-alignment, and figure-generation result trees, which can be regenerated from the released acquisition records using separately archived analysis code. The dataset can be reused for analysis of longitudinal potato root development, fluorescence-based bacterial colonisation, host-genotype × bacterial-strain interactions, and development or benchmarking of root- and fluorescence-image analysis workflows. Because both potato genotypes are represented under mock, WCS417-mCherry, and WCS358-mCherry conditions, the dataset also supports independent comparison of colonisation dynamics across the complete experimental design. In the companion methods study, WCS417 showed stronger colonisation of HYB007 than RP043, whereas WCS358 colonisation did not differ between the two host genotypes, illustrating the biological variation captured by the acquisition series. Exp35 provides the complete acquisition dataset underlying the potato root-colonisation experiment in the companion methods study, HADES: high-throughput end-to-end automation of multimodal phenotyping for root-microbe interactions. The experiment is presented in Supplementary Figure S3 and Supplementary Video S4, where longitudinal RootCam and fluorescence imaging are used to compare bacterial colonisation dynamics across potato genotypes and rhizobacterial strains. The complete experimental scope represented in the public Exp35 release corresponds to the experiment used in the methods study.