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Automatic 3D reconstruction of glia morphology is a powerful tool necessary for investigating the role of microglia in neurological disorders in the central nervous system. Current glia skeleton reconstruction techniques fail to capture an accurate tracing of the processes over time, useful for the study of the microglia motility and morphology in the brain during healthy and diseased states. We propose Hieroglyph, a fully automatic temporal 3D skeleton reconstruction algorithm for glia imaged via 3D multiphoton microscopy. Hieroglyph yielded a 21% performance increase compared to state of the art automatic skeleton reconstruction methods and outperforms the state of the art in different measures of consistency on datasets of 3D images of microglia. The results from this method provide a 3D graph and digital reconstruction of glia useful for a myriad of morphological analyses that could impact studies in brain immunology and disease., Comment: submitted to IEEE International Conference on Image Processing, 2019

We propose an automatic 3D segmentation algorithm for multiphoton microscopy images of microglia. Our method is capable of segmenting tubular and blob-like structures from noisy images. Current segmentation techniques and software fail to capture the fine processes and soma of the microglia cells, useful for the study of the microglia role in the brain during healthy and diseased states. Our coupled tubularity flow field (TuFF)-blob flow field (BFF) method evolves a level set toward the object boundary using the directional tubularity and blobness measure of 3D images. Our method found a 20% performance increase against state of the art segmentation methods on a dataset of 3D images of microglia even in images with intensity heterogeneity throughout the object. The coupled TuFF-BFF segmentation results also yielded 40% improvement in accuracy for the ramification index of the processes, which displays the efficacy of our method., submitted as a conference contribution to International Conference on Image Processing 2018