The lab has developed several tools or workflows in support of various aspects of proteomics data processing and analysis, as well as reagents in the course of our research. We provide details and links to these 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/

 

 

Reagents:

For work from our lab, we are making available plasmids through Addgene. If requesting viral reverse genetics plasmids, please contact Ed directly, as these are made available through MTA after confirming appropriate biosafety and GM approvals are in place.