PyPore3D: An Open Source Software Tool for Imaging Data Processing and Analysis of Porous and Multiphase Media

Abstract

In this work, we propose the software library PyPore3D, an open source solution for data processing of large 3D/4D tomographic data sets. PyPore3D is based on the Pore3D core library, developed thanks to the collaboration between Elettra Sincrotrone (Trieste) and the University of Trieste (Italy). The Pore3D core library is built with a distinction between the User Interface and the backend filtering, segmentation, morphological processing, skeletonisation and analysis functions. The current Pore3D version relies on the closed source IDL framework to call the backend functions and enables simple scripting procedures for streamlined data processing. PyPore3D addresses this limitation by proposing a full open source solution which provides Python wrappers to the the Pore3D C library functions. The PyPore3D library allows the users to fully use the Pore3D Core Library as an open source solution under Python and Jupyter Notebooks PyPore3D is both getting rid of all the intrinsic limitations of licensed platforms (e.g., closed source and export restrictions) and adding, when needed, the flexibility of being able to integrate scientific libraries available for Python (SciPy, TensorFlow, etc.).

Geochemistry and Petrology of the Bellecombe Lava Sequence, Enclos Fouqué Caldera, Piton de la Fournaise Volcano (Réunion, France)

“…Image analysis was performed by selecting a representative volume of interest of each sample from the original 3D images and extracting the vesicle phase using the manual thresholding approach of Fijii software [55]. The quantification of the bubble amount and morphology was then performed using the PyPore3D software library [56]. The 3D visualization of the images was obtained by the commercial software VGStudio MAX 2.0 (Volume Graphics).…”