Dataset Information

LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens.

ABSTRACT: Premise:Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time. Here, we present LeafMachine, an application designed to autonomously measure leaves from digitized herbarium specimens or leaf images using an ensemble of machine learning algorithms. Methods and Results:We trained LeafMachine on 2685 randomly sampled specimens from 138 herbaria and evaluated its performance on specimens spanning 20 diverse families and varying widely in resolution, quality, and layout. LeafMachine successfully extracted at least one leaf measurement from 82.0% and 60.8% of high- and low-resolution images, respectively. Of the unmeasured specimens, only 0.9% and 2.1% of high- and low-resolution images, respectively, were visually judged to have measurable leaves. Conclusions:This flexible autonomous tool has the potential to vastly increase available trait information from herbarium specimens, and inform a multitude of evolutionary and ecological studies.

SUBMITTER: Weaver WN

PROVIDER: S-EPMC7328653 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens.

Weaver William N WN Ng Julienne J Laport Robert G RG

Applications in plant sciences 20200601 6

<h4>Premise</h4>Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time. Here, we present LeafMachine, an application designed to autonomously measure leaves from digitized herbarium specimens or leaf images using an ensemble of machine learning algorithms.<h4>Methods and results</h4>We trained LeafMachine on 2685 randomly sampled specimens from 138 herbaria and evaluated its performance on ...[more]

PMID: 32626609

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Project description:Phenology-the timing of life-history events-is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual specimens, however, greatly restricts our ability to scale-up data collection. Recent investigations have demonstrated that machine-learning approaches can facilitate this effort. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., presence/absence of flowers). Here, we use crowd-sourced phenological data of buds, flowers, and fruits from >3,000 specimens of six common wildflower species of the eastern United States (Anemone canadensis L., A. hepatica L., A. quinquefolia L., Trillium erectum L., T. grandiflorum (Michx.) Salisb., and T. undulatum Wild.) to train models using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of each of the three reproductive stages with >87% accuracy. We also successfully estimated the relative abundance of each reproductive structure on a specimen with ≥90% accuracy. Precise counting of features was also successful, but accuracy varied with phenological stage and taxon. Specifically, counting flowers was significantly less accurate than buds or fruits likely due to their morphological variability on pressed specimens. Moreover, our Mask R-CNN model provided more reliable data than non-expert crowd-sourcers but not botanical experts, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, thus providing high-quality data with which to investigate plant responses to ongoing climatic change.

Project description:PurposeTo develop an objective and automated method for measuring intraocular pressure using deep learning and fixed-force Goldmann applanation tonometry (GAT) techniques.DesignProspective cross-sectional study.ParticipantsPatients from an academic glaucoma practice.MethodsIntraocular pressure was estimated by analyzing videos recorded using a standard slit-lamp microscope and fixed-force GAT. Video frames were labeled to identify the outline of the reference tonometer and the applanation mires. A deep learning model was trained to localize and segment the tonometer and mires. Intraocular pressure values were calculated from the deep learning-predicted tonometer and mire diameters using the Imbert-Fick formula. A separate test set was collected prospectively in which standard and automated GAT measurements were collected in random order by 2 independent masked observers to assess the deep learning model as well as interobserver variability.Main outcome measuresIntraocular pressure measurements between standard and automated methods were compared.ResultsTwo hundred sixty-three eyes of 135 patients were included in the training and validation videos. For the test set, 50 eyes from 25 participants were included. Each eye was measured by 2 observers, resulting in 100 videos. Within the test set, the mean difference between automated and standard GAT results was -0.9 mmHg (95% limits of agreement [LoA], -5.4 to 3.6 mmHg). Mean difference between the 2 observers using standard GAT was 0.09 mmHg (LoA,-3.8 to 4.0 mmHg). Mean difference between the 2 observers using automated GAT videos was -0.3 mmHg (LoA, -4.1 to 3.5 mmHg). The coefficients of repeatability for automated and standard GAT were 3.8 and 3.9 mmHg, respectively. The bias for even-numbered measurements was reduced when using automated GAT.ConclusionsPreliminary measurements using deep learning to automate GAT demonstrate results comparable with those of standard GAT. Automated GAT has the potential to improve on our current GAT measurement standards significantly by reducing bias and improving repeatability. In addition, ocular pulse amplitudes could be observed using this technique.

Dataset Information

LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens.

Publications

LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens.

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