PlaquePicker: Single-object based analysis of MSI data

Quantitative analysis of MSI datasets is typically performed on single pixels or manually assigned regions of interest (ROI). How-ever, many sparse, small objects such as Alzheimer’s disease (AD) brain deposits of amyloid peptides called plaques are neither single pixels nor ROI. Here, we propose a new approach to facilitate comparative computational evaluation of amyloid plaque-like objects by MSI: PLAQUE PICKER is a fast tool that enables statistical evaluation of heterogeneous amyloid peptide composition and other molecularly diverse sparsely-distributed features.

For more information about this package and its application on brains of mouse model for Alzheimer's disease please check our publication (

This package comes with a trimmed and reduced imzML data set as a example. If you would like to use the same data as in the paper: A mass spectrometry imaging data set for each of the used mouse models has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD020824.

CeMOS-Mannheim/PlaquePicker documentation built on Sept. 30, 2022, 5:54 a.m.