pomBseen: An automated pipeline for analysis of fission yeast images.
pomBseen: An automated pipeline for analysis of fission yeast images.
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DOI：
10.1371/journal.pone.0291391
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发表时间：
2023
期刊：
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
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作者：
裂殖酵母是一种广泛用于真核细胞生物学研究的模式生物。因此，它受到明场和荧光显微镜检查。对这些数据的手动分析可能是费力且主观的。因此，我们已经开发了pomBseen，一个图像分析管道，用于定量的裂变酵母显微照片包含一个明场通道和多达两个荧光通道。它接受广泛的图像格式，并生成一个表格，其中包含图像中细胞的大小、总荧光强度和细胞核荧光强度。针对手动注释的数据集对流水线进行基准测试表明，它可靠地分割细胞并获取其图像参数。pomBseen是用MATLAB编写的，也可以作为一个独立的应用程序使用。
Fission yeast is a model organism widely used for studies of eukaryotic cell biology. As such, it is subject to bright-field and fluorescent microscopy. Manual analysis of such data can be laborious and subjective. Therefore, we have developed pomBseen, an image analysis pipeline for the quantitation of fission yeast micrographs containing a bright-field channel and up to two fluorescent channels. It accepts a wide range of image formats and produces a table with the size and total and nuclear fluorescent intensities of the cells in the image. Benchmarking of the pipeline against manually annotated datasets demonstrates that it reliably segments cells and acquires their image parameters. Written in MATLAB, pomBseen is also available as a standalone application.