Reconstruction, analysis, and segmentation of LA-ICP-MS imaging data using Python for the identification of sub-organ regions in tissues

Abstract

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) imaging has been extensively used to determine the distributions of metals in biological tissues for a wide variety of applications. To be useful for identifying metal biodistributions, the acquired raw data needs to be reconstructed into a two-dimensional image. Several approaches have been developed for LA-ICP-MS image reconstruction, but less focus has been placed on software for more in-depth statistical processing of the imaging data. Yet, improved image processing can allow the biological ramifications of metal distributions in tissues to be better understood. In this work, we describe software written in Python that automatically reconstructs, analyzes, and segments images from LA-ICP-MS imaging data. Image segmentation is achieved using LA-ICP-MS signals from the biological metals Fe and Zn together with k-means clustering to automatically identify sub-organ regions in different tissues. Spatial awareness also can be incorporated into the images through a neighboring pixel evaluation that allows regions of interest to be identified that are at the limit of the LA-ICP-MS imaging resolution. The value of the described algorithms is demonstrated for LA-ICP-MS images of nanomaterial biodistributions. The developed image reconstruction and processing approach reveals that nanomaterials distribute in different sub-organ regions based on their chemical and physical properties, opening new possibilities for understanding the impact of such nanomaterials in vivo.