ArticlePlant physiology2009
HYPOTrace: image analysis software for measuring hypocotyl growth and shape demonstrated on Arabidopsis seedlings undergoing photomorphogenesis.
Article in Plant physiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 98 citations in OpenAlex.
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- APYRASE1/2 mediate red light-induced de-etiolation growth in Arabidopsis seedlings.Plant physiology · 2022Article
- Phenotyping Fusarium head blight through seed morphology characteristics using RGB imaging.Frontiers in plant science · 2022Article
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- High-resolution imaging as a tool for identifying quantitative trait loci that regulate photomorphogenesis inAoB PLANTS · 2021Article
- The microtubule-associated protein WDL4 modulates auxin distribution to promote apical hook opening in Arabidopsis.The Plant cell · 2021Article
- Assessment of root phenotypes in mungbean mini-core collection (MMC) from the World Vegetable Center (AVRDC) Taiwan.PloS one · 2021Article
- A Deep Learning-Based Approach for High-Throughput Hypocotyl Phenotyping.Plant physiology · 2019Article
- PI-Plat: a high-resolution image-based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits.Plant methods · 2019Article
- PlantSize Offers an Affordable, Non-destructive Method to Measure Plant Size and ColorFrontiers in plant science · 2018Article
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- LAZY Genes Mediate the Effects of Gravity on Auxin Gradients and Plant Architecture.Plant physiology · 2017Article
- ABCB19-mediated polar auxin transport modulates Arabidopsis hypocotyl elongation and the endoreplication variant of the cell cycle.The Plant journal : for cell and molecular biology · 2016Article
- 3D Surface Reconstruction of Plant Seeds by Volume Carving: Performance and Accuracies.Frontiers in plant science · 2016Article
- Advanced phenotyping and phenotype data analysis for the study of plant growth and development.Frontiers in plant science · 2015Review
- Dissecting the phenotypic components of crop plant growth and drought responses based on high-throughput image analysis.The Plant cell · 2014Article
- Integrated Analysis Platform: An Open-Source Information System for High-Throughput Plant Phenotyping.Plant physiology · 2014Article
- Advanced imaging techniques for the study of plant growth and development.Trends in plant science · 2014Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of time series of images can quantify plant growth and development, including the effects of genetic mutations (phenotypes) that give information about gene function. Here is demonstrated a software application named HYPOTrace that automatically extracts growth and shape information from electronic gray-scale images of Arabidopsis (Arabidopsis thaliana) seedlings. Key to the method is the iterative application of adaptive local principal components analysis to extract a set of ordered midline points (medial axis) from images of the seedling hypocotyl. Pixel intensity is weighted to avoid the medial axis being diverted by the cotyledons in areas where the two come in contact. An intensity feature useful for terminating the midline at the hypocotyl apex was isolated in each image by subtracting the baseline with a robust local regression algorithm. Applying the algorithm to time series of images of Arabidopsis seedlings responding to light resulted in automatic quantification of hypocotyl growth rate, apical hook opening, and phototropic bending with high spatiotemporal resolution. These functions are demonstrated here on wild-type, cryptochrome1, and phototropin1 seedlings for the purpose of showing that HYPOTrace generated expected results and to show how much richer the machine-vision description is compared to methods more typical in plant biology. HYPOTrace is expected to benefit seedling development research, particularly in the photomorphogenesis field, by replacing many tedious, error-prone manual measurements with a precise, largely automated computational tool.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.