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First, a small subset of the images ( yellow frame in Fig 2a) is imported as a new scene into an existing Cinema 4D project and the images from the raw data are loaded. Noise is removed with a non-local means filter (Fig 2b). The subimages are thresholded into a tentative segmentation of pores (black), aggregates (blue) and garnet (red). After this tentative segmentation, all other images from the raw data set are loaded as a new scene and another tentative segmentation is performed (Fig 2c). Global thresholding leads to a tentative segmentation into pores (black), aggregates (blue) and garnet (red). Partially overlapping particles are removed by erosion and removal of small objects (Fig 2d). Additionally, the edges of large garnet particles are masked out with a morphological dilation. The combination of erosion, removal of small objects and dilation removes false particle fragments and domains of pore voxels due to partial volume effects. The tentative segmentation results are improved with a Laplacian of Gaussian (LoG) filter (Fig 2e). The LoG filter is applied to all soil samples with the same settings as in the case study of Fig 1. By means of blob detection and a combination of erosion, removal of small objects and dilation, the LoG filter is able to detect garnet particles. The LoG segmentation in Fig 2e is compared to the LoG segmentation in Fig 1e. A very good correspondence can be seen.
The workflow as depicted in Fig 1 is applied to all soil samples of a double-labeled experiment. After image processing, each sample is analyzed in terms of the distribution of contact distance values between particles and pores. The contact distances are computed by a linear interpolation between voxel labeled as particle and its nearest neighbor labeled as pore. For each image in a sample, over 100 contact distance values are computed and assessed for the distribution of means, variances, skewness and kurtosis. The contact distance distributions are statistically analyzed and compared to established distributions of soil structure attributes. The following sections will discuss the individual steps of the image analysis workflow. The detailed description of the individual steps can be found in S1 File. An excerpt of the workflow for a case study from a silty loam soil is shown in Fig 2.
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