The lab has developed several tools or workflows in support of various aspects of proteomics data processing and analysis. We provide details and links to these tools below:

 

scpImaging

The scpImaging R package hex sticker

 

scpImaging is an R package and workflow for processing, analysing, and interactively visualising micrographs generated as part of cellenONE-based single-cell preparations, in our use case, for single-cell proteomics. It offers a first means of doublet detection for single-cell proteomics, as well as cell phenotyping convering cellenONE-based SCP experiments into multi-modal analyses. It also includes a custom iSEE panel, allowing for interactive visualisation of cells when using the bioconductor SCP package-based workflows.

 

Screen capture showing an iSEE app containing a cellenONEplot for visualising micrographs prepared by a cellenONE instrument.

 

Preprint – Loi, Holmes et al. (2025) Single-cell phenotypic analysis and multiplet detection through incorporation of microscopy data into cellenONE-based single-cell proteomics data analysis. bioRxiv.

Github – https://github.com/emmottlab/scpImaging

Try it online yourself – https://emmottlab.shinyapps.io/scpImaging_HEKA549/