Automated muscle histopathology analysis using CellProfiler.
Automated muscle histopathology analysis using CellProfiler.
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DOI：
10.1186/s13395-018-0178-6
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发表时间：
2018-10-18
期刊：
影响因子：
4.9
通讯作者：
Han R
中科院分区：
文献类型：
--
作者：
Lau YS;Xu L;Gao Y;Han R
骨骼肌切片的组织学评价对于肌肉生理和疾病的研究具有重要意义。骨骼肌的可量化测量通常包括平均纤维直径、纤维尺寸分布和中央有核肌纤维。这些参数提供了在与许多肌肉疾病和损伤相关的退化和再生的重复周期期间骨骼肌细胞的动态适应的见解。设计用于获得这些参数的计算程序将极大地促进这种努力，并提供优于人工图像分析的显著优势，人工图像分析是非常劳动密集型的并且通常是主观的。在这里，我们描述了一个定制的管道称为肌肉分析仪肌肉组织学分析的基础上CellProfiler，一个免费的，开源的软件，用于测量和分析细胞图像。MuscleAnalyzer管道包括加载、调整和运行CellProfiler提供的一系列图像处理模块。使用用层粘连蛋白（用于划分肌纤维边界）和4′，6-二脒基-2-苯基吲哚（DAPI，用于标记细胞核）共染色的野生型和mdx肌肉切片评价该管道。使用MuscleAnalyzer pipeline或手动分析的免疫荧光图像在mdx小鼠中每个图像的肌纤维数量（p = 0.42）和中央有核纤维（CNF）百分比（p = 0.29）方面产生了相似的结果。然而，对于总共67张图像，CellProfiler在常规PC上大约10分钟内完成了分析，而研究者使用手动方法需要大约3小时才能量化肌纤维和CNF的数量。此外，MuscleAnalyzer管道还提供了肌纤维横截面积（CSA）和最小Feret直径（MFD）的测量，从而可以绘制纤维尺寸分布。我们的数据表明，MuscleAnalyzer流水线可以以批处理格式有效准确地分析层粘连蛋白和DAPI共染色的肌肉图像，并提供肌肉组织学特性的定量测量，如肌纤维直径，纤维尺寸分布和CNF百分比。本文的在线版本（10.1186/s13395-018-0178-6）包含补充材料，可供授权用户使用。
Histological assessment of skeletal muscle sections is important for the research of muscle physiology and diseases. Quantifiable measures of skeletal muscle often include mean fiber diameter, fiber size distribution, and centrally nucleated muscle fibers. These parameters offer insights into the dynamic adaptation of skeletal muscle cells during repeated cycles of degeneration and regeneration associated with many muscle diseases and injuries. Computational programs designed to obtain these parameters would greatly facilitate such efforts and offer significant advantage over manual image analysis, which is very labor-intensive and often subjective. Here, we describe a customized pipeline termed MuscleAnalyzer for muscle histology analysis based upon CellProfiler, a free, open-source software for measuring and analyzing cell images. The MuscleAnalyzer pipeline consists of loading, adjusting, and running a series of image-processing modules provided by CellProfiler. This pipeline was evaluated using wild-type and mdx muscle sections co-stained with laminin (to demarcate the muscle fiber boundaries) and 4′,6-diamidino-2-phenylindole (DAPI, to label the nuclei). The immunofluorescence images analyzed using the MuscleAnalyzer pipeline or manually yielded similar results in the number of muscle fibers per image (p = 0.42) and central nucleated fiber (CNF) percentage (p = 0.29) in mdx mice. However, for a total of 67 images, CellProfiler completed the analysis in ~ 10 min on a regular PC while it took an investigator ~ 3 h using the manual approach in order to quantify the number of muscle fibers and CNF. Moreover, the MuscleAnalyzer pipeline also provided the measurement of the cross-sectional area (CSA) and minimal Feret’s diameter (MFD) of muscle fibers, and thus fiber size distribution can be plotted. Our data indicate that the MuscleAnalyzer pipeline can efficiently and accurately analyze laminin and DAPI co-stained muscle images in a batch format and provide quantitative measurements for muscle histological properties such as muscle fiber diameters, fiber size distribution, and CNF percentage. The online version of this article (10.1186/s13395-018-0178-6) contains supplementary material, which is available to authorized users.
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影响因子：
3.3
作者：
Liu, Fujun;Fry, Christopher S.;Yang, Lin
通讯作者：
Yang, Lin
影响因子：
12.3
作者：
Carpenter AE;Jones TR;Lamprecht MR;Clarke C;Kang IH;Friman O;Guertin DA;Chang JH;Lindquist RA;Moffat J;Golland P;Sabatini DM
通讯作者：
Sabatini DM
影响因子：
1.2
作者：
Pallafacchina, Giorgia;Francois, Stephanie;Buckingham, Margaret
通讯作者：
Buckingham, Margaret
影响因子：
4.9
作者：
Smith LR;Barton ER
通讯作者：
Barton ER
影响因子：
1
作者：
Papadopulos, Francesca;Spinelli, Matthew;Pasquinelli, Gianandrea
通讯作者：
Pasquinelli, Gianandrea