Back to Search
Start Over
Image Harvest: an open-source platform for high-throughput plant image processing and analysis
- Source :
- Journal of Experimental Botany
- Publication Year :
- 2016
- Publisher :
- Oxford University Press (OUP), 2016.
-
Abstract
- Highlight Image Harvest is an open-source software for high-throughput image processing and analysis that is integrated with the Open Science Grid and provides computational resources to process large image datasets.<br />High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources required for processing large image datasets at no cost. Image Harvest also offers functionalities to extract digital traits from images to interpret plant architecture-related characteristics. To demonstrate the applications of these digital traits, a rice (Oryza sativa) diversity panel was phenotyped and genome-wide association mapping was performed using digital traits that are used to describe different plant ideotypes. Three major quantitative trait loci were identified on rice chromosomes 4 and 6, which co-localize with quantitative trait loci known to regulate agronomically important traits in rice. Image Harvest is an open-source software for high-throughput image processing that requires a minimal learning curve for plant biologists to analyzephenomics datasets.
- Subjects :
- Crops, Agricultural
0106 biological sciences
0301 basic medicine
Physiology
Computer science
open-source software
ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION
Image processing
Plant Science
large-scale biology
Bioinformatics
computer.software_genre
01 natural sciences
Bottleneck
03 medical and health sciences
Phenomics
image analysis
Open Science Grid
Image Processing, Computer-Assisted
OpenCV
High-throughput computing
2. Zero hunger
Electronic Data Processing
High throughput computing
Oryza
Pipeline (software)
image processing
Metadata
Phenotype
030104 developmental biology
Parallel processing (DSP implementation)
phenomics
Feature (computer vision)
Data mining
computer
Software
Genome-Wide Association Study
Research Paper
010606 plant biology & botany
Subjects
Details
- ISSN :
- 14602431 and 00220957
- Volume :
- 67
- Database :
- OpenAIRE
- Journal :
- Journal of Experimental Botany
- Accession number :
- edsair.doi.dedup.....90b88452cde01357c34df3ea9660f39d