Organ-level instance segmentation enables continuous time-space-spectrum analysis of pre-clinical abdominal photoacoustic tomography images

Photoacoustic tomography (PAT), as a novel biomedical imaging technique, is able to capture temporal, spatial and spectral tomographic information from organisms. Organ-level multi-parametric analysis of continuous PAT images are of interest since it enables the quantification of organ specific morphological and functional parameters in small animals. Accurate organ delineation is imperative for organ-level image analysis, yet the low contrast and blurred organ boundaries in PAT images pose challenge for their precise segmentation. Fortunately, shared structural information among continuous images in the time-space-spectrum domain may be used to enhance segmentation. In this paper, we introduce a structure fusion enhanced graph convolutional network (SFE-GCN), which aims at automatically segmenting major organs including the body, liver, kidneys, spleen, vessel and spine of abdominal PAT image of mice. SFE-GCN enhances the structural feature of organs by fusing information in continuous image sequence captured at time, space and spectrum domains. As validated on large-scale datasets across different imaging scenarios, our method not only preserves fine structural details but also ensures anatomically aligned organ contours. Most importantly, this study explores the application of SFE-GCN in multi-dimensional organ image analysis, including organ-based dynamic morphological analysis, organ-wise light fluence correction and segmentation-enhanced spectral un-mixing. Code will be released at https://github.com/lzc-smu/SFEGCN.git.