Ice cores of polar regions (ice sheets) are one of the most prominent natural archives that can reveal essential historical information from the past environment of our planet. The ice core microstructure is a key feature in determining the principal properties of ice such as pore close-off, albedo, and melt events. Micro-CT scans can provide valuable information about the microstructure of materials, although achieving a high-quality automated segmentation of porous materials, especially with phase/density changes is still a challenge. This work proposes a new method for improving the segmentation of porous microstructures where a weak segmentation (Gaussian Mixture Model) on high-resolution (30 μm) data is used as ground truth to train a deep learning model (U-net) for segmentation of low-resolution (60 μm) data. This approach has reached high segmentation accuracy in terms of quantitative metrics having the F1-score of 92.5% and an intersection over the union of 91%, with a considerable improvement compared to thresholding and unsupervised methods. Also, the segmentation results of U-net are closer to the real weight, density, and specific surface area of the specimen.