This repository supplements the manuscript titled “Analyzing dynamics of metabolism in kidney repair at single-cell resolution”, which presents a method for dynamic analysis of metabolism on tissues at single-cell resolution using MALDI mass spectrometry imaging (MALDI-MSI). The manuscript is currently under revision. For a detailed description of the method, validation and application of this method in both mouse sham and IRI kidneys, please read our manuscript. Here we present the codes used for data analysis in this manuscript.