OPEN leaf : an open‐source cloud‐based phenotyping system for tracking dynamic changes at leaf‐specific resolution in Arabidopsis

Abstract

The first draft of the Arabidopsis genome was released more than 20 years ago and despite intensive molecular research, more than 30% of Arabidopsis genes remained uncharacterized or without an assigned function. This is in part due to gene redundancy within gene families or the essential nature of genes, where their deletion results in lethality (i.e., the dark genome). High-throughput plant phenotyping (HTPP) offers an automated and unbiased approach to characterize subtle or transient phenotypes resulting from gene redundancy or inducible gene silencing; however, access to commercial HTPP platforms remains limited. Here we describe the design and implementation of OPEN leaf, an open-source phenotyping system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing. OPEN leaf, coupled with our SMART imaging processing pipeline was able to consistently document and quantify dynamic changes at the whole rosette level and leaf-specific resolution when plants experienced changes in nutrient availability. Our data also demonstrate that VIS sensors remain underutilized and can be used in high-throughput screens to identify and characterize previously unidentified phenotypes in a leaf-specific time-dependent manner. Moreover, the modular and open-source design of OPEN leaf allows seamless integration of additional sensors based on users and experimental needs.

Plant phenotyping relevance

OPEN leafは、葉単位の動的表現型を取得・定量するオープンソース撮像プラットフォームと画像処理パイプラインの設計・実装を主題としており、植物フェノタイピング手法が中心である。

Code and data availability

The paper's SMART image-analysis pipeline (used for all rosette and leaf-specific phenotyping measurements in this study) is explicitly stated to be publicly available as source code on GitHub and as a prepackaged Docker container, with authors' URLs given in the text.