In a uniform layer consisting of a mixture of granular material and liquid, it is known that desiccation cracks exhibit various anisotropic patterns that depend on the nature of the shaking that the layer experienced before drying. The existence of this effect implies that information regarding the direction of shaking is retained as a kind of memory in the arrangements of granular particles. In this work, we made measurements in paste composed of Lycopodium powder using micro-focus X-ray computerized tomography (µCT) in order to investigate the 3-d arrangements of particles. We found shaking-induced anisotropic arrangements of neighboring particles and density fluctuations forming interstices mainly in the lower part of the layer. We compare the observed properties of these arrangements with numerical results obtained in the study of a model of non-Brownian particles under shear deformation. In the experimental system, we also observed crack tips in the µCT images and confirmed that these cracks grow along interstices in the direction perpendicular to the initial shaking.