CystAnalyser: A new software tool for the automatic detection and quantification of cysts in Polycystic Kidney and Liver Disease, and other cystic disorders.
CystAnalyser: A new software tool for the automatic detection and quantification of cysts in Polycystic Kidney and Liver Disease, and other cystic disorders.
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DOI：
10.1371/journal.pcbi.1008337
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发表时间：
2020-10
影响因子：
4.3
通讯作者：
García-González MA
中科院分区：
文献类型：
--
作者：
Cordido A;Cernadas E;Fernández-Delgado M;García-González MA
多囊肾病（PKD）的特征是进行性肾囊肿发展和其他肾外表现，包括多囊肝病（PLD）。通常使用模拟人类疾病的动物模型的表型表征，以研究新的分子机制并确定新的治疗方法。疾病进展的主要生物标志物是人和小鼠的肾脏和肝脏的总体积，其与器官功能相关。因此，估计囊肿占据的组织的数量和面积对于理解疾病的生理机制至关重要。在这方面，囊性指数是通常用于量化疾病严重程度的稳健参数。迄今为止，绝大多数生物医学研究人员使用ImageJ作为软件工具，通过量化阈值化后组织学图像的囊性面积来估计囊性指数。该工具具有不准确的模仿，主要是由于不正确地识别非囊性区域。我们开发了一种名为CystAnalyser的新软件（由Universidade de圣地亚哥de Compostela-USC和Fundación Investigación Sanitaria de Compostela-FIDIS注册），该软件将自动图像处理与图形用户友好界面相结合，使研究人员能够在量化之前监督并轻松纠正图像处理。CystAnalyser能够生成囊肿特征，包括囊肿指数、囊肿数量和囊肿大小。为了测试CystAnalyser软件，分析了795个囊性肾和肝组织学图像。使用CystAnalyser，自动计算囊性指数与用户输入没有差异，除非在特定情况下，用户需要区分轻度囊性和非囊性区域。通过自动定量检测的囊肿数量的灵敏度和特异性取决于器官类型和囊肿严重程度，肾脏的值为76.84-78.59%和76.96-89.66%，肝脏的值为87.29-93.80%和63.42-86.07%。此外，CystAnalyser提供了一种新的工具，用于估计囊肿数量和比ImageJ更具体的囊性指数测量。CystAnalyser是一种新的强大且可免费下载的软件工具，用于通过量化囊性器官的组织学图像来分析疾病的严重程度，用于常规生物医学研究。CystAnalyser可从https://citius.usc.es/transferencia/software/cystanalyser下载（适用于Windows和Linux），用于研究目的。这项工作表明CystAnalyser是目前可用于评估囊性病变（包括多囊肾病（PKD）和多囊肝病（PLD））的最可靠的软件工具。CystAnalyser将自动囊肿识别与友好的图形用户界面相结合，允许用户在组织学图像量化之前输入。CystAnalyser满足了获得PKD和PLD疾病进展的通用生物标志物Cystic指数（组织总面积内的囊肿面积）的可靠测量的需求。该软件工具还能够从组织学图像计算囊肿的数量和大小。总之，我们的结果表明，CystAnalyser克服了使用迄今为止最常用的软件（ImageJ）进行囊性指数定量检测的精度问题，为用户提供了一个可靠的工具，可以在使用动物模型的临床前研究中轻松表征PKD和PLD的表型和病理生理学。
The Polycystic Kidney Disease (PKD) is characterized by progressive renal cyst development and other extrarenal manifestation including Polycystic Liver Disease (PLD). Phenotypical characterization of animal models mimicking human diseases are commonly used, in order to, study new molecular mechanisms and identify new therapeutic approaches. The main biomarker of disease progression is total volume of kidney and liver in both human and mouse, which correlates with organ function. For this reason, the estimation of the number and area of the tissue occupied by cysts, is critical for the understanding of physiological mechanisms underlying the disease. In this regard, cystic index is a robust parameter commonly used to quantify the severity of the disease. To date, the vast majority of biomedical researchers use ImageJ as a software tool to estimate the cystic index by quantifying the cystic areas of histological images after thresholding. This tool has imitations of being inaccurate, largely due to incorrectly identifying non-cystic regions. We have developed a new software, named CystAnalyser (register by Universidade de Santiago de Compostela–USC, and Fundación Investigación Sanitaria de Santiago—FIDIS), that combines automatic image processing with a graphical user friendly interface that allows investigators to oversee and easily correct the image processing before quantification. CystAnalyser was able to generate a cystic profile including cystic index, number of cysts and cyst size. In order to test the CystAnalyser software, 795 cystic kidney, and liver histological images were analyzed. Using CystAnalyser there were no differences calculating cystic index automatically versus user input, except in specific circumstances where it was necessary for the user to distinguish between mildly cystic from non-cystic regions. The sensitivity and specificity of the number of cysts detected by the automatic quantification depends on the type of organ and cystic severity, with values 76.84–78.59% and 76.96–89.66% for the kidney and 87.29–93.80% and 63.42–86.07% for the liver. CystAnalyser, in addition, provides a new tool for estimating the number of cysts and a more specific measure of the cystic index than ImageJ. This study proposes CystAnalyser is a new robust and freely downloadable software tool for analyzing the severity of disease by quantifying histological images of cystic organs for routine biomedical research. CystAnalyser can be downloaded from https://citius.usc.es/transferencia/software/cystanalyser (for Windows and Linux) for research purposes. This work suggests CystAnalyser is the most reliable software tool currently available for the assessment of cystic pathologies including Polycystic Kidney Disease (PKD) and Polycystic Liver Disease (PLD). CystAnalyser combines automatic cyst recognition with a friendly graphical user interface, allowing user input prior to histological image quantification. CystAnalyser responds to the need to obtain reliable measurements of the universal biomarker for PKD and PLD disease progression, the Cystic index (area of cysts within the total area of tissue). This software tool is also able to calculate the number and size of cysts from the histological images. In summary, our results show that CystAnalyser overcomes the precision issues detected using the most commonly used software to date (ImageJ) for Cystic index quantification, offering users a reliable tool to easily characterize the phenotype and the pathophysiology of PKD and PLD in pre-clinical studies using animal models.
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影响因子：
10.5
作者：
Harris PC;Torres VE
通讯作者：
Torres VE
影响因子：
15.9
作者：
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DOI：
10.2215/cjn.10360818
发表时间：
2019-06-07
影响因子：
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作者：
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通讯作者：
Harris, Peter C.
影响因子：
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作者：
Hoevenaren, Inge A.;Wester, Ruth;Everson, Gregory T.
通讯作者：
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