A public-domain image processing tool for automated quantification of fluorescence in situ hybridisation signals
A public-domain image processing tool for automated quantification of fluorescence in situ hybridisation signals
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DOI：
10.1136/jcp.2007.048991
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发表时间：
2008-03-01
影响因子：
3.4
通讯作者：
Isola, J.
中科院分区：
文献类型：
--
作者：
Konsti, J.;Lundin, J.;Isola, J.
目的：建立和评价HER2荧光原位杂交（FISH）信号的自动定量方法。方法：利用流行的开源图像处理工具ImageJ，创建FISH信号评估宏。对来自42例乳腺癌患者的标本进行了与传统手工计数的比较。将肿瘤标本与HER2和17号染色体着丝粒（CEP17）探针杂交，并对选定区域进行数字化图像处理。使用ImageJ自定义宏手动和自动计算杂交信号。结果：自动与手动HER2/CEP17比值的相关系数为0.98。对应的一致性百分比为90%，kappa值为0.82。结论：本研究表明，使用开源软件自动化测定HER2扩增是可能的，其结果与人工计数相当。自动计数减少了样品分析所需的时间，并提供了提高实验室间和实验室内结果可重复性的可能性。FISH量化工具（FishJ）可以作为ImageJ宏下载，也可以通过一个带有上传FISH图像用于杂交信号计数选项的web界面来使用。结合FISH样本的数字化，FishJ宏可以在数字化样本的任何区域评估和重新评估基因拷贝数。
Aims: To develop and evaluate an automated method for quantification of HER2 fluorescence in situ hybridisation ( FISH) signals.Methods: Using a popular, open source image manipulation tool, ImageJ, a macro for FISH signal assessment was created. A comparison against traditional manual counting was performed in breast cancer specimens from 42 patients. The tumour specimens were hybridised with probes for HER2 and chromosome 17 centromere (CEP17) and selected areas were digitised for image processing. Hybridisation signals were calculated both manually and automatically with the ImageJ custom macro.Results: The correlation coefficient between the automatic and manual HER2/CEP17 ratios was 0.98. The corresponding percentage agreement was 90% and the kappa value was 0.82.Conclusions: This study shows that it is possible to automate the determination of HER2 amplification by the use of open-source software, with results comparable to manual counting. The automated counting decreases the time needed for sample analysis and provides possibilities to enhance inter- and intralaboratory reproducibility of results. The FISH quantification tool (FishJ) is available for download as an ImageJ macro or alternatively it can be utilised through a web interface with an option of uploading FISH images for hybridisation signal counting. Combined with digitisation of FISH samples, the FishJ macro enables gene copy number to be assessed and reevaluated on any area of a digitised specimen.