In plant-fungus phenotyping, determining fungal hyphal and plant root lengths by digital image analysis can reduce labour and increase data reproducibility. However, the degree of software sophistication is often prohibitive and manual measuring is still used, despite being very time-consuming. We developed the HyLength tool for measuring the lengths of hyphae and roots in in vivo and in vitro systems. The HyLength was successfully validated against manual measures of roots and fungal hyphae obtained from all systems. Compared with manual methods, the HyLength underestimated Medicago sativa roots in the in vivo system and Rhizophagus irregularis hyphae in the in vitro system by about 12 cm per m and allowed to save about 1 h for a single experimental unit. As regards hyphae of R. irregularis in the in vivo system, the HyLength overestimated the length by about 21 cm per m compared with manual measures, but time saving was up to 20.5 h per single experimental unit. Finally, with hyphae of Aspergillus oryzae, the underestimation was about 8 cm per m with a time saving of about 10 min for a single germinating spore. By benchmarking the HyLength against the AnaMorf plugin of the ImageJ/Fiji, we found that the HyLength performed better for dense fungal hyphae, also strongly reducing the measuring time. The HyLength can allow measuring the length over a whole experimental unit, eliminating the error due to sub-area selection by the user and allowing processing a high number of samples. Therefore, we propose the HyLength as a useful freeware tool for measuring fungal hyphae of dense mycelia.

中文翻译：

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HyLength：一种半自动数字图像分析工具，用于测量致密菌丝的根部长度和真菌菌丝。

在植物-真菌表型中，通过数字图像分析确定真菌菌丝和植物根的长度可以减少工作量并提高数据可重复性。但是，软件复杂性的程度通常是令人望而却步的，尽管非常耗时，但仍然使用手动测量。我们开发了HyLength工具，用于测量体内和体外系统中的菌丝和根的长度。该HyLength成功验证对根和所有系统获得的真菌菌丝的人工措施。与人工方法相比，HyLength在体内系统和不规则根瘤菌中低估了紫花苜蓿的根体外系统中的菌丝每米约12厘米，单个实验单元可节省约1小时。关于体内系统中的不规则红杆菌的菌丝，HyLength与人工测量相比高估了每米21厘米的长度，但每个实验单元最多可节省20.5小时的时间。最后，用米曲霉的菌丝，低估为每米约8厘米，单个发芽孢子可节省约10分钟的时间。通过将HyLength与ImageJ / Fiji的AnaMorf插件进行基准测试，我们发现HyLength对浓密的真菌菌丝表现更好，也大大减少了测量时间。所述HyLength可以允许测量在整个实验单元的长度，消除了错误，由于由所述用户子区域选择，并允许处理大量的样品。因此，我们建议将HyLength作为有用的免费软件工具，用于测量致密菌丝体的真菌菌丝。