Using CellProfiler to Analyze and Quantify Vascular Morphology.

Abstract

Computational programs can be used in place of time-consuming, error-prone manual data collection. CellProfiler is a free, open source program that allows researchers to automate image analysis and collect large amounts of phenotypic data relatively easily. Here, we describe how to adapt CellProfiler to analyze cross sections of xylem tissue and use it to gather a variety of information on traits such as cell size, shape, and number. We provide step-by-step instructions to create a typical CellProfiler analysis pipeline, alongside explanations of important modules, options and parameters available to the user.

Plant phenotyping relevance

CellProfilerを用いて木部横断面画像から細胞サイズ・形状・数を抽出する解析パイプラインを開発・解説しており、植物形態形質の取得方法が中心である。

Code and data availability

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