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X-ray micro-computed tomography (X-ray micro-CT) is widely employed to investigate flow phenomena in porous media, providing a powerful alternative to core-scale experiments for estimating traditional petrophysical properties such as porosity, single-phase permeability or fluid connectivity. However, the segmentation process, critical for deriving these properties from greyscale images, varies significantly between studies due to the absence of a standardized workflow or any ground truth data. This introduces challenges in comparing results across different studies, especially for properties sensitive to segmentation. To address this, we present a fully open-source, automated workflow for the segmentation of a Bentheimer sandstone filled with nitrogen and brine. The workflow incorporates a traditional image processing pipeline, including non-local means filtering, image registration, watershed segmentation of grains, and a combination of differential imaging and thresholding for segmentation of the fluid phases. Our workflow enhances reproducibility by enabling other research groups to easily replicate and validate findings, fostering consistency in petrophysical property estimation. Moreover, its modular structure facilitates integration into modeling frameworks, allowing for forward-backward communication and parameter sensitivity analyses. We apply the workflow to exploring the sensitivity of the non-wetting phase volume, surface area, and connectivity to image processing. This adaptable tool paves the way for future advancements in X-ray micro-CT analysis of porous media.