Quanfima: An open source Python package for automated fiber analysis of biomaterials

Hybrid 3D scaffolds composed of different biomaterials with fibrous structure or enriched with different inclusions (i.e., nano- and microparticles) have already demonstrated their positive effect on cell integration and regeneration. The analysis of fibers in hybrid biomaterials, especially in a 3D space is often difficult due to their various diameters (from micro to nanoscale) and compositions. Though biomaterials processing workflows are implemented, there are no software tools for fiber analysis that can be easily integrated into such workflows. Due to the demand for reproducible science with Jupyter notebooks and the broad use of the Python programming language, we have developed the new Python package quanfima offering a complete analysis of hybrid biomaterials, that include the determination of fiber orientation, fiber and/or particle diameter and porosity. Here, we evaluate the provided tensor-based approach on a range of generated datasets under various noise conditions. Also, we show its application to the X-ray tomography datasets of polycaprolactone fibrous scaffolds pure and containing silicate-substituted hydroxyapatite microparticles, hydrogels enriched with bioglass contained strontium and alpha-tricalcium phosphate microparticles for bone tissue engineering and porous cryogel 3D scaffold for pancreatic cell culturing. The results obtained with the help of the developed package demonstrated high accuracy and performance of orientation, fibers and microparticles diameter and porosity analysis.

由不同生物材料制备、具有纤维结构，或负载不同内含物（即纳米与微米颗粒）的混合三维支架，已被证实可有效促进细胞整合与组织再生。然而，由于纤维的直径跨度覆盖微米至纳米尺度且组成各异，对混合生物材料中的纤维进行分析——尤其是在三维空间环境下——往往颇具难度。尽管当前已建立成熟的生物材料加工流程，但目前尚无可轻松集成至此类流程的专用纤维分析软件工具。鉴于科研可重复性对Jupyter笔记本（Jupyter Notebook）的需求，以及Python编程语言的广泛应用，我们开发了全新Python包quanfima，可实现混合生物材料的完整分析，涵盖纤维取向、纤维及/或颗粒直径与孔隙率的测定。本研究针对多种噪声条件下生成的多组数据集，对所提出的基于张量的分析方法进行了评估。此外，我们还展示了该方法在以下X射线断层扫描（X-ray Tomography）数据集上的应用：纯聚己内酯纤维支架及负载硅酸盐取代羟基磷灰石微米颗粒的聚己内酯纤维支架、用于骨组织工程的负载含锶生物玻璃与α-磷酸三钙微米颗粒的水凝胶，以及用于胰腺细胞培养的多孔冷冻凝胶三维支架。借助该开发工具包所得的分析结果证实，该方法在纤维取向、纤维与微米颗粒直径及孔隙率分析方面具备极高的准确度与性能表现。