组织分析:用于心脏器官样品研究的多功能图像预处理与分析软件。
Organalysis: Multifunctional Image Preprocessing and Analysis Software for Cardiac Organoid Studies.
发表日期:2023 Sep 06
作者:
Jathin Pranav Singaraju, Adheesh Kadiresan, Rahul Kumar Bhoi, Angello Huerta Gomez, Zhen Ma, Huaxiao Yang
来源:
Stem Cell Research & Therapy
摘要:
鉴于近期干细胞研究领域对人类多能干细胞源器官模型的可视化需求日益增长,一个高效的批量处理应用程序是必要的,以提供预处理和图像分析服务。在本研究中,我们开发了一种名为Organalysis的高精度、多功能和易用的应用程序,以满足这些需求,提供图像处理和增强功能、器官模型面积和强度计算、分形分析、噪声去除和特征重要性计算等功能。图像处理功能包括亮度和对比度调整。面积和强度计算为每个图像计算了六个值:器官模型面积、总图像面积、图像被器官模型覆盖的百分比、器官模型的总强度、器官模型按面积计算的总强度,以及器官模型总强度与总图像面积的总和。分形分析功能计算了每个图像的分形维度值。噪声去除功能从输入图像中去除多余的标记,如气泡和其他不需要的噪声。特征重要性功能通过训练一个Lasso正则化线性回归机器学习算法,来识别对细胞分化最重要的心脏生长因子。该应用程序的批量处理功能进一步建立在现有的ImageJ服务的基础上,提供了一种更方便的处理多幅图像的方式。Organalysis的多功能和精确性共同表明其创新性,因为目前没有其他图像处理软件能够同时具备批量处理和广泛的特征分析能力。因此,Organalysis在心脏器官模型研究中提供了独特的功能,其在再生医学领域的价值不可估量。
Due to a growing need in visualizing human pluripotent stem cell-derived organoids from recent advancements in the field, an efficient bulk-processing application is necessary to providing preprocessing and image analysis services. In this study, we developed Organalysis, a high-accuracy, multifunctional, and accessible application that meets these needs by providing functionality of image manipulation and enhancement, organoid area and intensity calculation, fractal analysis, noise removal, and feature importance computation. The image manipulation feature includes brightness and contrast adjustment. The area and intensity calculation computes six values for each image: organoid area, total image area, percentage of the image covered by organoid, total intensity of organoid, total intensity of organoid-by-organoid area, and total intensity of organoid by total image area. The fractal analysis function computes the fractal dimension value for each image. The noise removal function removes superfluous marks from the input images, such as bubbles and other unwanted noise. The feature importance function trains a lasso-regularized linear regression machine learning algorithm to identify cardiac growth factors that are the strongest determinants for cell differentiation. The batch processing of this application further builds on existing services like ImageJ to provide a more convenient way to process multiple images. Collectively, the versatility and preciseness of Organalysis demonstrate novelty, since no other current imaging software combines the capability of batch processing and the breadth of feature analysis. Therefore, Organalysis provides unique functions in cardiac organoid research and proves to be invaluable in regenerative medicine.