Benjamin A. Lloyd, Richard S. Barclay, Regan E. Dunn, Ellen D. Currano, Ayuni I. Mohamaad, Kymbre Skersies, Surangi W. Punyasena
Premise
Leaf epidermal cell morphology is closely tied to the evolutionary history of plants and their growth environments and is therefore of interest to many plant biologists. However, cell measurement can be time consuming and restrictive with current methods. CuticleTrace is a suite of Fiji and R-based functions that streamlines and automates the segmentation and measurement of epidermal pavement cells across a wide range of cell morphologies and image qualities.
Methods and Results
We evaluated CuticleTrace-generated measurements against those from alternate automated methods and expert and undergraduate hand tracings across a taxonomically diverse 50-image data set of variable image qualities. We observed ~93% statistical agreement between CuticleTrace and expert hand-traced measurements, outperforming alternate methods.
Conclusions
CuticleTrace is a broadly applicable, modular, and customizable tool that integrates data visualization and cell shape measurement with image segmentation, lowering the barrier to high-throughput studies of epidermal morphology by vastly decreasing the labor investment required to generate high-quality cell shape data sets.
{"title":"CuticleTrace: A toolkit for capturing cell outlines from leaf cuticle with implications for paleoecology and paleoclimatology","authors":"Benjamin A. Lloyd, Richard S. Barclay, Regan E. Dunn, Ellen D. Currano, Ayuni I. Mohamaad, Kymbre Skersies, Surangi W. Punyasena","doi":"10.1002/aps3.11566","DOIUrl":"https://doi.org/10.1002/aps3.11566","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Leaf epidermal cell morphology is closely tied to the evolutionary history of plants and their growth environments and is therefore of interest to many plant biologists. However, cell measurement can be time consuming and restrictive with current methods. CuticleTrace is a suite of Fiji and R-based functions that streamlines and automates the segmentation and measurement of epidermal pavement cells across a wide range of cell morphologies and image qualities.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We evaluated CuticleTrace-generated measurements against those from alternate automated methods and expert and undergraduate hand tracings across a taxonomically diverse 50-image data set of variable image qualities. We observed ~93% statistical agreement between CuticleTrace and expert hand-traced measurements, outperforming alternate methods.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>CuticleTrace is a broadly applicable, modular, and customizable tool that integrates data visualization and cell shape measurement with image segmentation, lowering the barrier to high-throughput studies of epidermal morphology by vastly decreasing the labor investment required to generate high-quality cell shape data sets.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11566","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139750068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this study, we use simulations to determine how pollen flow and sampling constraints can influence the genetic conservation found in seed collections.
Methods
We simulated genotypes of parental individuals and crossed the parentals based on three different ranges of pollen flow (panmictic, limited, and highly limited) to create new seed sets for sampling. We tested a variety of sampling scenarios modeled on those occurring in nature and calculated the proportion of alleles conserved in each scenario.
Results
We found that pollen flow greatly influences collection outcomes, with panmictic pollen flow resulting in seed sets containing 21.6% more alleles than limited pollen flow and 48.6% more alleles than highly limited pollen flow, although this impact diminishes when large numbers of maternal plants are sampled. Simulations of realistic seed sampling (sampling more seed from some plants and fewer from others) showed a relatively minor impact (<2.5%) on genetic diversity conserved compared to ideal sampling (uniform sampling across all maternal plants).
Discussion
We conclude that future work must consider limited pollen flow, but collectors can be flexible with their sampling in the field as long as many unique maternal plants are sampled. Simulations remain a fruitful method to advance ex situ sampling guidelines.
在这项研究中，我们通过模拟来确定花粉流动和取样限制如何影响种子采集中的遗传保护。
{"title":"Simulating pollen flow and field sampling constraints helps revise seed sampling recommendations for conserving genetic diversity","authors":"Kaylee J. Rosenberger, Sean Hoban","doi":"10.1002/aps3.11561","DOIUrl":"10.1002/aps3.11561","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>In this study, we use simulations to determine how pollen flow and sampling constraints can influence the genetic conservation found in seed collections.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We simulated genotypes of parental individuals and crossed the parentals based on three different ranges of pollen flow (panmictic, limited, and highly limited) to create new seed sets for sampling. We tested a variety of sampling scenarios modeled on those occurring in nature and calculated the proportion of alleles conserved in each scenario.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We found that pollen flow greatly influences collection outcomes, with panmictic pollen flow resulting in seed sets containing 21.6% more alleles than limited pollen flow and 48.6% more alleles than highly limited pollen flow, although this impact diminishes when large numbers of maternal plants are sampled. Simulations of realistic seed sampling (sampling more seed from some plants and fewer from others) showed a relatively minor impact (<2.5%) on genetic diversity conserved compared to ideal sampling (uniform sampling across all maternal plants).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We conclude that future work must consider limited pollen flow, but collectors can be flexible with their sampling in the field as long as many unique maternal plants are sampled. Simulations remain a fruitful method to advance ex situ sampling guidelines.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11561","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139662266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Natália Mossmann Koch, Raúl Díaz Dominguez, Ana Fávaro, Daniel Stanton
Premise
Methods to evaluate lichen thalli hydrophobicity have previously been described, but only recently has hydrophobicity been shown to be an important functional trait related to water regulation dynamics that could be used to predict future climate change effects. We describe a novel protocol to measure lichen thallus hydrophobicity that aims to be an easier and more affordable approach.
Methods and Results
Our protocol requires only a micropipette, distilled water, a tripod, and a smartphone or camera. Hydrophobicity is inferred from multiple metrics associated with the absorption times of standardized droplets (initial and total absorption time). We used a data set of 93 lichen taxa with different growth forms and from different biomes and demonstrated that this method is well suited for capturing different levels of hydrophobicity, including very hydrophilic species.
Conclusions
Our results show that this new protocol to measure lichen hydrophobicity is a rapid and low-cost method to assess an ecophysiologically based functional trait that can be used with almost no limitations, including in different climates, lichen species, and growth forms.
{"title":"Thallus hydrophobicity: A low-cost method for understanding lichen ecophysiological responses to environmental changes","authors":"Natália Mossmann Koch, Raúl Díaz Dominguez, Ana Fávaro, Daniel Stanton","doi":"10.1002/aps3.11565","DOIUrl":"10.1002/aps3.11565","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Methods to evaluate lichen thalli hydrophobicity have previously been described, but only recently has hydrophobicity been shown to be an important functional trait related to water regulation dynamics that could be used to predict future climate change effects. We describe a novel protocol to measure lichen thallus hydrophobicity that aims to be an easier and more affordable approach.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Our protocol requires only a micropipette, distilled water, a tripod, and a smartphone or camera. Hydrophobicity is inferred from multiple metrics associated with the absorption times of standardized droplets (initial and total absorption time). We used a data set of 93 lichen taxa with different growth forms and from different biomes and demonstrated that this method is well suited for capturing different levels of hydrophobicity, including very hydrophilic species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our results show that this new protocol to measure lichen hydrophobicity is a rapid and low-cost method to assess an ecophysiologically based functional trait that can be used with almost no limitations, including in different climates, lichen species, and growth forms.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11565","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139587663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Erika R. Moore-Pollard, Daniel S. Jones, Jennifer R. Mandel
Premise
A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization.
Methods
We developed a Hyb-Seq probe set, Compositae-ParaLoss-1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 Packera taxa that were previously studied using Compositae-1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support.
Results
We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae-1061. Most notably, Compositae-ParaLoss-1272 recovered substantially fewer paralogous sequences than Compositae-1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae-1061.
Discussion
Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae-ParaLoss-1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.
{"title":"Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems","authors":"Erika R. Moore-Pollard, Daniel S. Jones, Jennifer R. Mandel","doi":"10.1002/aps3.11568","DOIUrl":"10.1002/aps3.11568","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We developed a Hyb-Seq probe set, Compositae-ParaLoss-1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus <i>Packera</i>. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 <i>Packera</i> taxa that were previously studied using Compositae-1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae-1061. Most notably, Compositae-ParaLoss-1272 recovered substantially fewer paralogous sequences than Compositae-1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae-1061.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae-ParaLoss-1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11568","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139587590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae.
Methods
In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version.
Results
The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery.
Discussion
This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant-targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.
{"title":"An updated and extended version of the Melastomataceae probe set for target capture","authors":"Léo-Paul M. J. Dagallier, Fabián A. Michelangeli","doi":"10.1002/aps3.11564","DOIUrl":"10.1002/aps3.11564","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant-targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11564","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139495487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ryan A. Folk, Robert P. Guralnick, Raphael T. LaFrance
Premise
Plant trait data are essential for quantifying biodiversity and function across Earth, but these data are challenging to acquire for large studies. Diverse strategies are needed, including the liberation of heritage data locked within specialist literature such as floras and taxonomic monographs. Here we report FloraTraiter, a novel approach using rule-based natural language processing (NLP) to parse computable trait data from biodiversity literature.
Methods
FloraTraiter was implemented through collaborative work between programmers and botanical experts and customized for both online floras and scanned literature. We report a strategy spanning optical character recognition, recognition of taxa, iterative building of traits, and establishing linkages among all of these, as well as curational tools and code for turning these results into standard morphological matrices.
Results
Over 95% of treatment content was successfully parsed for traits with <1% error. Data for more than 700 taxa are reported, including a demonstration of common downstream uses.
Conclusions
We identify strategies, applications, tips, and challenges that we hope will facilitate future similar efforts to produce large open-source trait data sets for broad community reuse. Largely automated tools like FloraTraiter will be an important addition to the toolkit for assembling trait data at scale.
{"title":"FloraTraiter: Automated parsing of traits from descriptive biodiversity literature","authors":"Ryan A. Folk, Robert P. Guralnick, Raphael T. LaFrance","doi":"10.1002/aps3.11563","DOIUrl":"10.1002/aps3.11563","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Plant trait data are essential for quantifying biodiversity and function across Earth, but these data are challenging to acquire for large studies. Diverse strategies are needed, including the liberation of heritage data locked within specialist literature such as floras and taxonomic monographs. Here we report FloraTraiter, a novel approach using rule-based natural language processing (NLP) to parse computable trait data from biodiversity literature.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>FloraTraiter was implemented through collaborative work between programmers and botanical experts and customized for both online floras and scanned literature. We report a strategy spanning optical character recognition, recognition of taxa, iterative building of traits, and establishing linkages among all of these, as well as curational tools and code for turning these results into standard morphological matrices.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Over 95% of treatment content was successfully parsed for traits with <1% error. Data for more than 700 taxa are reported, including a demonstration of common downstream uses.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>We identify strategies, applications, tips, and challenges that we hope will facilitate future similar efforts to produce large open-source trait data sets for broad community reuse. Largely automated tools like FloraTraiter will be an important addition to the toolkit for assembling trait data at scale.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139495519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mason C. McNair, Sebastian C. Cocioba, Peter Pietrzyk, Trevor W. Rife
Premise
Low-cost, repairable lab equipment is rare within the biological sciences. By lowering the costs of entry using 3D printing and open-source hardware, our goal is to empower both amateur and professional scientists to conduct research.
Methods
We developed a modular system of 3D-printable designs called COBLE (Collection of Bespoke Laboratory Equipment), including novel and remixed 3D-printable lab equipment that can be inexpensively printed, assembled, and repaired for a fraction of the cost of retail equivalents.
Results
Here we present novel tools that utilize 3D printing to enable a wide range of scientific experiments. We include additional resources for scientists and labs that are interested in utilizing 3D printing for their research.
Discussion
By describing the broad potential that 3D-printed designs can have in the biological sciences, we hope to inspire others to implement and improve upon these designs, improving accessibility and enabling science for all.
低成本、可维修的实验室设备在生物科学领域非常罕见。通过使用 3D 打印和开源硬件降低入门成本，我们的目标是让业余和专业科学家都能开展研究。
{"title":"Toward an open-source 3D-printable laboratory","authors":"Mason C. McNair, Sebastian C. Cocioba, Peter Pietrzyk, Trevor W. Rife","doi":"10.1002/aps3.11562","DOIUrl":"10.1002/aps3.11562","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Low-cost, repairable lab equipment is rare within the biological sciences. By lowering the costs of entry using 3D printing and open-source hardware, our goal is to empower both amateur and professional scientists to conduct research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We developed a modular system of 3D-printable designs called COBLE (Collection of Bespoke Laboratory Equipment), including novel and remixed 3D-printable lab equipment that can be inexpensively printed, assembled, and repaired for a fraction of the cost of retail equivalents.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Here we present novel tools that utilize 3D printing to enable a wide range of scientific experiments. We include additional resources for scientists and labs that are interested in utilizing 3D printing for their research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>By describing the broad potential that 3D-printed designs can have in the biological sciences, we hope to inspire others to implement and improve upon these designs, improving accessibility and enabling science for all.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11562","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139515161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Robert Guralnick, Raphael LaFrance, Michael Denslow, Samantha Blickhan, Mark Bouslog, Sean Miller, Jenn Yost, Jason Best, Deborah L. Paul, Elizabeth Ellwood, Edward Gilbert, Julie Allen
Premise
Among the slowest steps in the digitization of natural history collections is converting imaged labels into digital text. We present here a working solution to overcome this long-recognized efficiency bottleneck that leverages synergies between community science efforts and machine learning approaches.
Methods
We present two new semi-automated services. The first detects and classifies typewritten, handwritten, or mixed labels from herbarium sheets. The second uses a workflow tuned for specimen labels to label text using optical character recognition (OCR). The label finder and classifier was built via humans-in-the-loop processes that utilize the community science Notes from Nature platform to develop training and validation data sets to feed into a machine learning pipeline.
Results
Our results showcase a >93% success rate for finding and classifying main labels. The OCR pipeline optimizes pre-processing, multiple OCR engines, and post-processing steps, including an alignment approach borrowed from molecular systematics. This pipeline yields >4-fold reductions in errors compared to off-the-shelf open-source solutions. The OCR workflow also allows human validation using a custom Notes from Nature tool.
Discussion
Our work showcases a usable set of tools for herbarium digitization including a custom-built web application that is freely accessible. Further work to better integrate these services into existing toolkits can support broad community use.
{"title":"Humans in the loop: Community science and machine learning synergies for overcoming herbarium digitization bottlenecks","authors":"Robert Guralnick, Raphael LaFrance, Michael Denslow, Samantha Blickhan, Mark Bouslog, Sean Miller, Jenn Yost, Jason Best, Deborah L. Paul, Elizabeth Ellwood, Edward Gilbert, Julie Allen","doi":"10.1002/aps3.11560","DOIUrl":"10.1002/aps3.11560","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Among the slowest steps in the digitization of natural history collections is converting imaged labels into digital text. We present here a working solution to overcome this long-recognized efficiency bottleneck that leverages synergies between community science efforts and machine learning approaches.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We present two new semi-automated services. The first detects and classifies typewritten, handwritten, or mixed labels from herbarium sheets. The second uses a workflow tuned for specimen labels to label text using optical character recognition (OCR). The label finder and classifier was built via humans-in-the-loop processes that utilize the community science Notes from Nature platform to develop training and validation data sets to feed into a machine learning pipeline.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our results showcase a >93% success rate for finding and classifying main labels. The OCR pipeline optimizes pre-processing, multiple OCR engines, and post-processing steps, including an alignment approach borrowed from molecular systematics. This pipeline yields >4-fold reductions in errors compared to off-the-shelf open-source solutions. The OCR workflow also allows human validation using a custom Notes from Nature tool.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our work showcases a usable set of tools for herbarium digitization including a custom-built web application that is freely accessible. Further work to better integrate these services into existing toolkits can support broad community use.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11560","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139372778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jamie R. Sykes, Katherine J. Denby, Daniel W. Franks
Plant pathogens can decimate crops and render the local cultivation of a species unprofitable. In extreme cases this has caused famine and economic collapse. Timing is vital in treating crop diseases, and the use of computer vision for precise disease detection and timing of pesticide application is gaining popularity. Computer vision can reduce labour costs, prevent misdiagnosis of disease, and prevent misapplication of pesticides. Pesticide misapplication is both financially costly and can exacerbate pesticide resistance and pollution. Here, we review the application and development of computer vision and machine learning methods for the detection of plant disease. This review goes beyond the scope of previous works to discuss important technical concepts and considerations when applying computer vision to plant pathology. We present new case studies on adapting standard computer vision methods and review techniques for acquiring training data, the use of diagnostic tools from biology, and the inspection of informative features. In addition to an in-depth discussion of convolutional neural networks (CNNs) and transformers, we also highlight the strengths of methods such as support vector machines and evolved neural networks. We discuss the benefits of carefully curating training data and consider situations where less computationally expensive techniques are advantageous. This includes a comparison of popular model architectures and a guide to their implementation.
{"title":"Computer vision for plant pathology: A review with examples from cocoa agriculture","authors":"Jamie R. Sykes, Katherine J. Denby, Daniel W. Franks","doi":"10.1002/aps3.11559","DOIUrl":"10.1002/aps3.11559","url":null,"abstract":"<p>Plant pathogens can decimate crops and render the local cultivation of a species unprofitable. In extreme cases this has caused famine and economic collapse. Timing is vital in treating crop diseases, and the use of computer vision for precise disease detection and timing of pesticide application is gaining popularity. Computer vision can reduce labour costs, prevent misdiagnosis of disease, and prevent misapplication of pesticides. Pesticide misapplication is both financially costly and can exacerbate pesticide resistance and pollution. Here, we review the application and development of computer vision and machine learning methods for the detection of plant disease. This review goes beyond the scope of previous works to discuss important technical concepts and considerations when applying computer vision to plant pathology. We present new case studies on adapting standard computer vision methods and review techniques for acquiring training data, the use of diagnostic tools from biology, and the inspection of informative features. In addition to an in-depth discussion of convolutional neural networks (CNNs) and transformers, we also highlight the strengths of methods such as support vector machines and evolved neural networks. We discuss the benefits of carefully curating training data and consider situations where less computationally expensive techniques are advantageous. This includes a comparison of popular model architectures and a guide to their implementation.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11559","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Morris, A. B., C. Scalf, A. Burleyson, L. T. Johnson, and K. Trostel. 2016. Development and characterization of microsatellite primers in the federally endangered Astragalus bibullatus (Fabaceae). Applications in Plant Sciences 4(4): e1500126.
In Table 1, the reverse primer sequences for loci Abib051, Abib156, and Abib170 were incorrect. Table 1 is provided here with the corrected sequences shown in boldface.
{"title":"Correction to Development and characterization of microsatellite primers in the federally endangered Astragalus bibullatus (Fabaceae)","authors":"","doi":"10.1002/aps3.11555","DOIUrl":"10.1002/aps3.11555","url":null,"abstract":"<p>Morris, A. B., C. Scalf, A. Burleyson, L. T. Johnson, and K. Trostel. 2016. Development and characterization of microsatellite primers in the federally endangered <i>Astragalus bibullatus</i> (Fabaceae). <i>Applications in Plant Sciences</i> 4(4): e1500126.</p><p>In Table 1, the reverse primer sequences for loci Abib051, Abib156, and Abib170 were incorrect. Table 1 is provided here with the corrected sequences shown in boldface.</p><p>We apologize for this error.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11555","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138526675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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