An automated quantitative image analysis tool for the identification of microtubule patterns in plants

Abstract

High throughput confocal imaging poses challenges in the computational image analysis of complex subcellular structures such as the microtubule cytoskeleton. Here, we developed CellArchitect, an automated image analysis tool that quantifies changes to subcellular patterns illustrated by microtubule markers in plants. We screened microtubule-targeted herbicides and demonstrate that high throughput confocal imaging with integrated image analysis by CellArchitect can distinguish effects induced by the known herbicides indaziflam and trifluralin. The same platform was used to examine 6 other compounds with herbicidal activity, and at least 3 different effects induced by these compounds were profiled. We further show that CellArchitect can detect subcellular patterns tagged by actin and endoplasmic reticulum markers. Thus, the platform developed here can be used to automate image analysis of complex subcellular patterns for purposes such as herbicide discovery and mode of action characterisation. The capacity to use this tool to quantitatively characterize cellular responses lends itself to application across many areas of biology.

The use of quantitative imaging to investigate regulators of membrane trafficking in Arabidopsis stomatal closure

“…However, the relationship between these processes is not well understood. Quantitative high‐throughput screening is a powerful approach to dissect membrane trafficking, and being quantitative and at single cell (or subcellular) resolution, overcoming lethality and redundancy issues . We present a quantitative image‐based screen in Arabidopsis thaliana to identify components of the endomembrane system involved in guard cell responses to five stimuli.…”

“…Quantitative high-throughput screening is a powerful approach to dissect membrane trafficking, and being quantitative and at single cell (or subcellular) resolution, overcoming lethality and redundancy issues. 12,35,36 We present a quantitative image-based screen in Arabidopsis thaliana to identify components of the endomembrane system involved in guard cell responses to five stimuli. Focussing our attention on RAB5 GTPases, a small gene family in A. thaliana, 37 we tested mutants in the conventional RAB5 GTPases A. thaliana RAB 7 (ARA7) and homologous RAB Homologue 1 (RHA1) as well as the plant-unique RAB5 GTPase ARA6 in restricting bacterial invasion as well as their effect on FLS2 endocytosis.…”

Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat

“…choosing traits based on the statistical variation or dispersion of a set of phenotypic data values. Whilst implementing the software, we built on our previous work in batch processing and high-throughput trait analysis [ 56 , 63 , 64 ] and improved software implementation in areas such as reducing computational complexity (e.g. the usage of CPU cores and memory in parallel computing), optimising data annotation and data exchange between application programming interfaces (APIs), i.e.…”

Leaf-GP: An Open and Automated Software Application for Measuring Growth Phenotypes for Arabidopsis and Wheat

“…choosing traits based on the statistical variation or dispersion of a set of phenotypic data values. Whilst implementing the software, we built on our previous work in batch processing and high-throughput trait analysis [52–56] and improved software implementation in areas such as reducing computational complexity (e.g. the usage of CPU cores and memory in parallel computing), optimising data annotation and data exchange between application programming interfaces (APIs), i.e.…”