Seethepalli et al. 2024 bioRxiv
Divide and conquer: Using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods
Anand Seethepalli, Chanae Ottley, Joanne Childs, Kevin Cope, Aubrey K. Fine, John Lagergren, Colleen M. Iversen, Udaya Kalluri, Larry M. York
July 10, 2024, BioRxiv; DOI:10.1101/2024.07.05.602287
Abstract
Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. The collection of root samples from the field and their subsequent cleaning and scanning in a water-filled tray ranging in size from 5 to 20 cm, followed by digital image analysis has been commonly used since the 1990s for measuring root length, volume, area, and diameter. However, one common issue has been neglected. Sometimes, the amount of roots for a sample is too much to fit into a single scanned image, so the sample is divided among several scans. There is no standard method to aggregate the root measurements across the scans of the same sample. Here, we describe and validate two methods for standardizing measurements across multiple scans: image concatenation and statistical aggregation. Both methods rely on standardizing file naming conventions to identify scans that belong to the same sample. Image concatenation refers to combining digital images into a single larger image while maintaining the original resolution. We developed a Python script that identifies which images belong to the same sample and returns a single, larger concatenated image for every set of images in a directory. These concatenated images (combining up to 10 scans) and the original images were processed with RhizoVision Explorer, a free and open-source software developed for estimating root traits from images, with the same settings. An R script was developed that can identify the rows of data belonging to the same sample in RhizoVision Explorer data files and apply correct statistical methods such as summation, weighted average by length, and average to the appropriate measurement types to return a single data row for each sample. These two methods were compared using example images from switchgrass, poplar, and various tree and ericaceous shrub species from a northern peatland and the Arctic. Overall, the new methods accomplished the goal of standardizing measurement aggregation. Most root measurements were nearly identical except median diameter, which can not be accurately computed by statistical aggregation. We believe the availability of these methods will be useful to the root biology community.
Citation
Seethepalli A, Ottley C, Childs J, Cope K, Fine AK, Lagergren J, Iversen CM, Kalluri U, York LM (2024). Divide and conquer: Using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods. BioRxiv 14, 12983. DOI: 10.1101/2024.07.05.602287
