Engineering topics

Childs, Joanne

Publications and source records attributed to Childs, Joanne.

3 records

DOE OSTI2024

SPRUCE Root Tip and Ectomycorrhizal Fungi Colonization Measurements from Ingrowth Cores, 2017

This data set contains root tip and ectomycorrhizal fungi colonization measurements taken from ingrowth cores from the SPRUCE experiment (Hanson et al. 2017) that were deployed during the 2017 growing season (2017-06 to 2017-10-01). This study explored the relationship between warming treatments and fine-root growth. Increased fine-root growth may increase root exudates and accelerate turnover, representing an underlying mechanism for peat decomposition through priming, as exudates provide a labile carbon source to the microbial community. Roots of two tree species were studied: an evergreen conifer Picea mariana (black spruce) and a deciduous conifer Larix laricina (tamarack). Measurements include root tips counts and densities by tree species and the abundance of ectomycorrhizal colonization on root tips. This dataset contains one data file in comma separate (.csv) format. Additional metadata are provided: one data dictionary and a file-level metadata file in comma separate (.csv) format and a user guide in PDF (*.pdf) format.

black spruce [Picea mariana]↗

DOE OSTI2024

Divide and conquer: using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods

Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. Sometimes, the amount of roots in a sample is too much to fit into a single scanned image, so the sample is divided among several scans, and there is no standard method to aggregate the data. Here, we describe and validate two methods for standardizing measurements across multiple scans: image concatenation and statistical aggregation. We developed a Python script that identifies which images belong to the same sample and returns a single, larger concatenated image. These concatenated images and the original images were processed with RhizoVision Explorer, a free and open-source software. An R script was developed, which identifies rows of data belonging to the same sample and applies correct statistical methods 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. Most root measurements were nearly identical between the two methods except median diameter, which cannot be accurately computed by statistical aggregation. We believe the availability of these methods will be useful to the root biology community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Variation in forest root image annotation by experts, novices, and AI

Abstract Background The manual study of root dynamics using images requires huge investments of time and resources and is prone to previously poorly quantified annotator bias. Artificial intelligence (AI) image-processing tools have been successful in overcoming limitations of manual annotation in homogeneous soils, but their efficiency and accuracy is yet to be widely tested on less homogenous, non-agricultural soil profiles, e.g., that of forests, from which data on root dynamics are key to understanding the carbon cycle. Here, we quantify variance in root length measured by human annotators with varying experience levels. We evaluate the application of a convolutional neural network (CNN) model, trained on a software accessible to researchers without a machine learning background, on a heterogeneous minirhizotron image dataset taken in a multispecies, mature, deciduous temperate forest. Results Less experienced annotators consistently identified more root length than experienced annotators. Root length annotation also varied between experienced annotators. The CNN root length results were neither precise nor accurate, taking ~ 10% of the time but significantly overestimating root length compared to expert manual annotation ( p = 0.01). The CNN net root length change results were closer to manual ( p = 0.08) but there remained substantial variation. Conclusions Manual root length annotation is contingent on the individual annotator. The only accessible CNN model cannot yet produce root data of sufficient accuracy and precision for ecological applications when applied to a complex, heterogeneous forest image dataset. A continuing evaluation and development of accessible CNNs for natural ecosystems is required.

Handy, Grace↗