SMASH - semi-automatic muscle analysis using segmentation of histology: a MATLAB application.
SMASH - semi-automatic muscle analysis using segmentation of histology: a MATLAB application.
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DOI：
10.1186/2044-5040-4-21
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发表时间：
2014
期刊：
影响因子：
4.9
通讯作者：
Barton ER
中科院分区：
文献类型：
--
作者：
Smith LR;Barton ER
骨骼肌组织的组织学评估通常应用于骨骼肌生理研究的许多领域。组织学参数，包括纤维分布、纤维类型、中央有核纤维和毛细血管密度，都是骨骼肌的常用量化指标。这些参数反映了肌肉的功能特性，并在许多肌肉疾病和损伤中经历适应。虽然已经开发了标准操作程序来指导许多这些参数的分析，但自由、高效和一致地分析它们的软件并不容易获得。为了向肌肉研究界提供这项服务，我们开发了一个开源 MATLAB 脚本来分析免疫荧光肌肉切片，并结合用户控件进行肌肉组织学分析。该软件由多种功能组成，旨在为所选分析提供工具。初始分割和纤维滤波器功能对图像进行分割，并根据用户定义的参数去除非纤维元素，以创建纤维掩模。根据用户设置的参数，软件输出有关纤维尺寸和类型、中心成核纤维和其他结构的数据。这些功能在 1 岁野生型和 mdx 小鼠（杜氏肌营养不良症模型）的染色比目鱼肌切片上进行了评估。根据之前发布的数据，各组之间的纤维尺寸没有差异，但 mdx 肌肉的纤维尺寸变异性要高得多。 mdx 肌肉中 I 型纤维的比例明显较高，但 I 型纤维相对于 II 型纤维的大小没有变化。中央有核纤维在 mdx 肌肉中非常普遍，并且明显大于外周有核纤维。随本手稿描述和提供的 MATLAB 代码专为骨骼肌免疫荧光组织学切片的图像处理而设计。该程序允许半自动光纤检测以及用户校正。代码的输出提供了符合既定实践标准的数据。该程序的结果已使用一小组野生型和 mdx 肌肉切片进行了验证。该程序是第一个免费提供的开源图像处理程序，旨在自动分析骨骼肌组织学切片。
Histological assessment of skeletal muscle tissue is commonly applied to many areas of skeletal muscle physiological research. Histological parameters including fiber distribution, fiber type, centrally nucleated fibers, and capillary density are all frequently quantified measures of skeletal muscle. These parameters reflect functional properties of muscle and undergo adaptation in many muscle diseases and injuries. While standard operating procedures have been developed to guide analysis of many of these parameters, the software to freely, efficiently, and consistently analyze them is not readily available. In order to provide this service to the muscle research community we developed an open source MATLAB script to analyze immunofluorescent muscle sections incorporating user controls for muscle histological analysis. The software consists of multiple functions designed to provide tools for the analysis selected. Initial segmentation and fiber filter functions segment the image and remove non-fiber elements based on user-defined parameters to create a fiber mask. Establishing parameters set by the user, the software outputs data on fiber size and type, centrally nucleated fibers, and other structures. These functions were evaluated on stained soleus muscle sections from 1-year-old wild-type and mdx mice, a model of Duchenne muscular dystrophy. In accordance with previously published data, fiber size was not different between groups, but mdx muscles had much higher fiber size variability. The mdx muscle had a significantly greater proportion of type I fibers, but type I fibers did not change in size relative to type II fibers. Centrally nucleated fibers were highly prevalent in mdx muscle and were significantly larger than peripherally nucleated fibers. The MATLAB code described and provided along with this manuscript is designed for image processing of skeletal muscle immunofluorescent histological sections. The program allows for semi-automated fiber detection along with user correction. The output of the code provides data in accordance with established standards of practice. The results of the program have been validated using a small set of wild-type and mdx muscle sections. This program is the first freely available and open source image processing program designed to automate analysis of skeletal muscle histological sections.
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