ISegMSI: An Interactive Strategy to Improve Spatial Segmentation of Mass Spectrometry Imaging Data

Lei Guo, Xingxing Liu, Chao Zhao, Zhenxing Hu, Xiangnan Xu, Kian Kai Cheng, Peng Zhou, Yu Xiao, Mudassir Shah, Jingjing Xu*, Jiyang Dong*, Zongwei Cai

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

7 Citations (Scopus)


Spatial segmentation is a critical procedure in mass spectrometry imaging (MSI)-based biochemical analysis. However, the commonly used unsupervised MSI segmentation methods may lead to inappropriate segmentation results as the MSI data is characterized by high dimensionality and low signal-to-noise ratio. This process can be improved by the incorporation of precise prior knowledge, which is hard to obtain in most cases. In this study, we show that the incorporation of partial or coarse prior knowledge from different sources such as reference images or biological knowledge may also help to improve MSI segmentation results. Here, we propose a novel interactive segmentation strategy for MSI data called iSegMSI, which incorporates prior information in the form of scribble-regularization of the unsupervised model to fine-tune the segmentation results. By using two typical MSI data sets (including a whole-body mouse fetus and human thyroid cancer), the present results demonstrate the effectiveness of the iSegMSI strategy in improving the MSI segmentations. Specifically, the method can be used to subdivide a region into several subregions specified by the user-defined scribbles or to merge several subregions into a single region. Additionally, these fine-tuned results are highly tolerant to the imprecision of the scribbles. Our results suggest that the proposed iSegMSI method may be an effective preprocessing strategy to facilitate the analysis of MSI data.

Original languageEnglish
Pages (from-to)14522-14529
Number of pages8
JournalAnalytical Chemistry
Issue number42
Early online date12 Oct 2022
Publication statusPublished - 25 Oct 2022

Scopus Subject Areas

  • Analytical Chemistry


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