IMPPY3D: Image Processing in Python for 3D Image Stacks.

Abstract

Image Processing in Python for 3D image stacks, or IMPPY3D, is a free and open-source software (FOSS) repository that simplifies post-processing and 3D shape characterization for grayscale image stacks, otherwise known as volumetric images, 3D images, or voxel models. While IMPPY3D, pronounced impee-three-dee, was originally created for post-processing image stacks generated from X-ray computed tomography (XCT) measurements, it can be applied generally in post-processing 2D and 3D images. IMPPY3D includes tools for segmenting volumetric images and characterizing the 3D shape of features or regions of interest. These functionalities have proven useful in 3D shape analysis of powder particles, porous polymers, concrete aggregates, internal pores/defects, and more (see the Research Applications section). IMPPY3D consists of a combination of original Python scripts, Cython extensions, and convenience wrappers for popular third-party libraries like SciKit-Image (Walt et al., 2014), OpenCV (Bradski, 2000), and PyVista (Sullivan & Kaszynski, 2019). Highlighted capabilities of IMPPY3D include: varying image processing parameters interactively, applying numerous 2D/3D image filters (e.g., blurring/sharpening, denoising, erosion/dilation), segmenting and labeling continuous 3D objects, precisely rotating and re-slicing an image stack in 3D, generating rotated bounding boxes fitted to voxelized features, converting image stacks into 3D voxel models, exporting 3D models as Visualization Toolkik (VTK) files for ParaView (Ayachit, 2015), and converting voxel models into smooth mesh-based models. Additional information and example scripts can be found in the included ReadMe files within the IMPPY3D GitHub repository (Moser, Landauer, et al., 2024). As a visualized example, Figure 1 demonstrates the high-level steps to characterize powder particles using IMPPY3D. This workflow is also similar to how pores can be visualized and characterized in metal-based additive manufacturing. Additional research applications for IMPPY3D are discussed in a later section.