Towards a more predictive community ecology: integrating functional traits and disequilibrium
Lead Research Organisation:
University of Oxford
Department Name: Geography - SoGE
Abstract
Imagine going to a garden store and buying every kind of vegetable seed packet for sale. Sow them all in a patch of bare ground, and then try to predict which particular species will be harvestable at the end of the season. Even the best ecological science is stymied by this simple challenge. An open problem is predicting or controlling the dynamics of communities, whether they are vegetable gardens or tropical forests.
The goal of this work is to develop biodiversity theory that can link across scales from individuals to communities to ecosystems. A more predictive ecological science could 1) delineate the processes and mechanisms that operate at or across different spatial scales and 2) generate falsifiable predictions for biodiversity dynamics in specific systems over time. To begin to address these aims, I will test two key ideas: first, that organisms' physiology needs to be built in to models of population growth; and second, that the matching between physiology and environment is not necessarily optimal, because of disequilibrium caused by lagged responses of organisms to rapid change. Over the next five years I will expand and test these ideas in a set of long-term study sites spanning the lowland tropics of Malaysia to the high alpine of Colorado.
The goal of this work is to develop biodiversity theory that can link across scales from individuals to communities to ecosystems. A more predictive ecological science could 1) delineate the processes and mechanisms that operate at or across different spatial scales and 2) generate falsifiable predictions for biodiversity dynamics in specific systems over time. To begin to address these aims, I will test two key ideas: first, that organisms' physiology needs to be built in to models of population growth; and second, that the matching between physiology and environment is not necessarily optimal, because of disequilibrium caused by lagged responses of organisms to rapid change. Over the next five years I will expand and test these ideas in a set of long-term study sites spanning the lowland tropics of Malaysia to the high alpine of Colorado.
Planned Impact
The primary beneficiaries of this work will be the international academic ecology community, as detailed under the 'Academic beneficiaries' subsection. Briefly, this work will provide a set of conceptual ideas and immediately usable models / software tools that will enable more robust thinking in community ecology.
The predictive modeling approaches pioneered by this proposal will provide benefits for land-management agencies and other groups interested in predicting or managing species' distributions under changing climates or external disturbance. Extrapolating species response to novel conditions remains an ongoing but highly practical challenge in ecology.
The project will also provide training and educational benefits for several students both in and out of the UK. The fieldwork in the United States, Malaysia, Ghana, and Peru will involve several local research assistants who will likely be masters' students from their respective countries. I will be able to provide additional training and international contacts for these students. Within the UK, I will supervise several students engaged in laboratory work to analyze samples collected for these projects. This work will provide valuable research experience that will increase these students' competitiveness for future jobs or research careers.
Lastly, the project will impact the public through engagement with this research. I will share photographs and short essays about my research through international photo competitions and my outreach blog (bblonder.wordpress.com). I have previously won several competitions and had images featured in journals such as BMC Ecology and newspapers such as The Guardian. My blog receives 20-50 visitors per day, primarily from Europe but also from a range of other countries.
The predictive modeling approaches pioneered by this proposal will provide benefits for land-management agencies and other groups interested in predicting or managing species' distributions under changing climates or external disturbance. Extrapolating species response to novel conditions remains an ongoing but highly practical challenge in ecology.
The project will also provide training and educational benefits for several students both in and out of the UK. The fieldwork in the United States, Malaysia, Ghana, and Peru will involve several local research assistants who will likely be masters' students from their respective countries. I will be able to provide additional training and international contacts for these students. Within the UK, I will supervise several students engaged in laboratory work to analyze samples collected for these projects. This work will provide valuable research experience that will increase these students' competitiveness for future jobs or research careers.
Lastly, the project will impact the public through engagement with this research. I will share photographs and short essays about my research through international photo competitions and my outreach blog (bblonder.wordpress.com). I have previously won several competitions and had images featured in journals such as BMC Ecology and newspapers such as The Guardian. My blog receives 20-50 visitors per day, primarily from Europe but also from a range of other countries.
Organisations
- University of Oxford (Lead Research Organisation)
- UNIVERSITY OF OXFORD (Collaboration)
- UNIVERSITY OF ABERDEEN (Collaboration)
- Los Alamos National Laboratory (Collaboration)
- Oregon State University (Collaboration)
- University of California, Merced (Collaboration)
- Norwegian University of Science and Technology (NTNU) (Collaboration)
- University of California, Berkeley (Fellow)
People |
ORCID iD |
| Benjamin Blonder (Principal Investigator / Fellow) |
Publications
Blonder B
(2018)
A model for leaf temperature decoupling from air temperature
in Agricultural and Forest Meteorology
Loranger J
(2016)
Occupancy and overlap in trait space along a successional gradient in Mediterranean old fields.
in American journal of botany
Blonder B
(2017)
Hypervolume concepts in niche- and trait-based ecology
in Ecography
Morueta-Holme N
(2016)
A network approach for inferring species associations from co-occurrence data
in Ecography
Blonder B
(2017)
Predicting trait-environment relationships for venation networks along an Andes-Amazon elevation gradient.
in Ecology
Aparecido LMT
(2020)
High water use in desert plants exposed to extreme heat.
in Ecology letters
Blonder B
(2017)
Predictability in community dynamics.
in Ecology letters
Gaüzère P
(2018)
Empirical Predictability of Community Responses to Climate Change
in Frontiers in Ecology and Evolution
Blonder B
(2018)
Extreme and Highly Heterogeneous Microclimates in Selectively Logged Tropical Forests
in Frontiers in Forests and Global Change
Blonder B
(2020)
Low predictability of energy balance traits and leaf temperature metrics in desert, montane and alpine plant communities
in Functional Ecology
| Title | Art show |
| Description | Organized community art show at Rocky Mountain Biological Laboratory in order to share scientific perspectives on art and creativity. Featured ~30 pieces of art from ~20 scientists/artists and engaged ~100 members of public and students. |
| Type Of Art | Artistic/Creative Exhibition |
| Year Produced | 2015 |
| Impact | Wide public interest and engagement from students |
| Title | Artistic/Creative Exhibition - RMBL art show 2017 (2017) |
| Description | Community-supported art show for scientists / public at Rocky Mountain Biological Laboratory |
| Type Of Art | Artwork |
| Year Produced | 2017 |
| Impact | Event featured > 30 artists and many students. Attendance > 100 people. Event fundraised ~1000 USD for field station. |
| Title | RMBL art show 2016 |
| Description | Organized community art show at Rocky Mountain Biological Laboratory in order to share scientific perspectives on art and creativity. Featured ~30 pieces of art from ~20 scientists/artists and engaged ~100 members of public and students. |
| Type Of Art | Artistic/Creative Exhibition |
| Year Produced | 2016 |
| Impact | Wide public engagement from students and scientists. Fostered conversations about diversity and inclusion in science as a result of some art pieces touching on these themes. |
| Description | I have successfully completed the major data objectives relevant to this grant, i.e. establishment and monitoring of long-term plant demography plots in the Colorado alpine zone, as well as intensive collection of functional traits in that Colorado site and in a disturbance gradient in Malaysian Borneo (datasets D1 and D2 of the Case for Support). These datasets have been analyzed answer Q3 of the proposal. I am developing theory for disequilibrium dynamics. I have published in American Naturalist a key paper sketching methods for inferring how invasions may occur in plant communities via 'holes' in niche or trait hypervolumes, and have also published another paper relevant to the theory of how traits mediate community assembly, published at Ecology, and another paper focused on how community composition (in terms of traits or niches) can track environmental change, or fail to, which is now published in Ecology Letters. Three other papers further develop concepts for community assembly based on niches. These projects address Q2 and Q4 of the proposal. Ongoing work I am leading is also using a range of empirical datasets to test some of these ideas, including plant ecophysiology data from Peru and Borneo, plant pollen assemblage timeseries from North America, contemporary plant community composition time series from North America, bird morphology data at global scale, and global-scale plant composition and paleoclimate time series data. These studies are ongoing and will address a range of questions relevant to how quickly communities can respond to climate change, how predictable their responses are, and whether organisms' traits are useful predictors of these responses. Three papers addressing Q4 have now been published. Separately I have published theory for leaf energy balance (addressing Q5) with an American collaborator, and another still in review. Other trait and microclimate data (also relevant to Q5) has now been collected from Borneo and are now published. This work has also supported research experiences for several students, including three co-supervised masters students (two of whom received a distinction last year for their finished theses), four summer undergraduate research students (both from under-represented Native American backgrounds). The overall impact in the three years of this grant is to have built much of the key theoretical apparatus to succeed with the grant's major objectives, and to have published several empirical studies testing theoretical predictions or demonstrating the utility of the grant's core ideas. Most of the key theory papers are out, and the major empirical datasets are now published. Additional projects relevant to the grant are largely completed and are in review at journals. I feel that the project's goals will be realized once these papers have been published. |
| Exploitation Route | The theory and concepts I am developing are likely to shape the way in which modeling of future climate change responses and species invasions will be carried out. These concepts/tools are implemented in freely available R software and can be easily made relevant. |
| Sectors | Agriculture, Food and Drink,Education,Environment |
| URL | http://www.benjaminblonder.org |
| Description | The pathways to impact funding is supporting at least 300 hours of environmental education teaching in the United States by a graduate student, and has also supported the development of an extensive set of inquiry-based environmental education resources to be shared and implemented in the US and UK. These materials have now been piloted with a group of 20-30 geography teacher trainees in the UK, 30 teachers in the USA, and are also being implemented this year in a series of two one-week programs reaching approximately 100 US-based students. Further curriculum development has supported the production of a guide to best practices in mentoring and inquiry-based teaching that will shortly be made publicly available, advertised to teachers, and presented at international meetings. As of 2023 we had a book accepted for publication by Routledge on place-based science education, the majority of whose content was developed by me during this award. This book is anticipated to have a large impact on secondary school education. |
| First Year Of Impact | 2023 |
| Sector | Education,Environment |
| Impact Types | Societal |
| Description | Teacher training |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Developed educational materials around inquiry-based science education suitable for use by secondary school teachers. Facilitated half-day or multi-day teacher training workshops (personally or via paid staff) in US and UK reaching approx. 50 teachers or teacher trainees. All materials will shortly be available online. |
| Description | Klimaforsk |
| Amount | kr 130,000 (NOK) |
| Organisation | Research Council of Norway |
| Sector | Public |
| Country | Norway |
| Start | 08/2015 |
| End | 08/2017 |
| Description | National Science Foundation |
| Amount | $997,000 (USD) |
| Organisation | National Science Foundation (NSF) |
| Sector | Public |
| Country | United States |
| Start | 01/2019 |
| End | 01/2023 |
| Description | Seed grant programme |
| Amount | £7,390 (GBP) |
| Organisation | University of Oxford |
| Department | John Fell Fund |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 12/2018 |
| Description | Small grants program |
| Amount | £5,000 (GBP) |
| Organisation | British Ecological Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2017 |
| End | 12/2018 |
| Description | Startup funding (new job after resigning fellowship) |
| Amount | $580,000 (USD) |
| Organisation | Arizona State University |
| Sector | Academic/University |
| Country | United States |
| Start | 01/2018 |
| End | 01/2020 |
| Title | Hypervolume |
| Description | Developed 'hypervolume' software (in R) that enables novel trait-based analyses for biological invasions, community assembly, species distribution modeling. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Underlies several high profile research articles in journals including Ecology Letters, PNAS, and Nature. Package updated via major methods paper in Methods In Ecology & Evolution in 2017. |
| URL | https://cran.r-project.org/web/packages/hypervolume/index.html |
| Title | Venation |
| Description | Software and algorithms to segment leaf venation network images. Currently further developing algorithms using convolutional neural network machine learning methods with Prof Mark Fricker and Hao Xu at Oxford. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Several research students and one international group (@ CNRS) now use these software tools to analyze their data. |
| URL | http://github.com/bblonder/venation_programs |
| Title | netassoc |
| Description | Software tool implemented in R to infer species associations for studies of community assembly and responses to climate change. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | Am aware of at least 2-3 other research groups actively using this tool for studies of community assembly in e.g. intertidal ecosystems. |
| URL | https://cran.r-project.org/web/packages/netassoc/index.html |
| Title | Alpine demography |
| Description | Plant demography and census data for 2000 individuals in 50 alpine plant communities in Colorado, as well as associated functional trait measurements for all species. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | These data are being paired with phenology measurements to support the PhD thesis of one student at Duke University in the USA. One publication in Journal of Ecology and one more in preparation. |
| Title | BALI microclimate |
| Description | Microclimate measurements at 20 minute resolution and 5m spatial resolution for a 1 month time interval for three distinct 1ha forest fragments in Malaysian Borneo |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | One publication in review. Data to be submitted to Dryad on acceptance. |
| Title | CHAMBASA traits |
| Description | Venation trait data for 130+ species on Andes/Amazon elevation gradient |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Supported 3 publications (see publications section of report) |
| Title | Data from: Linking microenvironment modification to species interactions and demography in an alpine plant community |
| Description | Individual plants can modify the microenvironment within their spatial neighborhood. However, the consequences of microenvironment modification for demography and species interactions remain unclear at the community scale. In a study of co-occurring alpine plants, we (1) determined the extent of species-specific microclimate modification by comparing temperature and soil moisture between vegetated and non-vegetated microsites for several focal species. We (2) determined how vital rates (survival, growth, fecundity) of all species varied in response to aboveground and belowground vegetative overlap with inter- and intraspecific neighbors as proxies for microenvironment modification. For (1), surface temperatures were buffered (lower maximums and higher minimums) and soil moisture was higher below the canopies of most species compared to non-vegetated areas. For (2), vegetative overlap predicted the most vital rates, although the effect varied depending on whether aboveground or belowground overlap was considered. Vital rate response to microenvironment-modification proxies (vegetative overlap) was also frequently context-dependent with respect to plant size and macroclimate. Microenvironment modification and spatial overlapping of individuals are key drivers of demography and species interactions in this alpine community. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | http://datadryad.org/stash/dataset/doi:10.6078/D1342B |
| Title | Leaf Vein Network CNN Images |
| Description | This download site contains the CNN vein network predictions and set of Matlab programs that were used for the analyses in Xu et al., (2020) and Blonder et al., (2020). These require Matlab 2020a or later. They may work on earlier versions of MatLab, but this has not been tested and cannot be guaranteed. The files are as follows: Zip files (e.g. BEL_downsampled_images.zip) containing a complete set of images of leaf vein predictions from a fully trained convolutional neural network (CNN), along with the ground truth data. Each folder in the unzipped file contains a sample represented by a CODE with format X-TY-BZ. X represents the name of a plot in the Global Ecosystems Monitoring network database (e.g. 'BEL'). Tree (T) Y indicates the number of a tree within a plot (e.g. '101') and Z represents the light stratum of the canopy where the leaf was collected (either 'S' for 'sunlit' or 'SH' for 'shaded'). A set of Matlab programs (Matlab files.zip) to compare the CNN predictions against other vein extraction approaches. A Matlab Readme file with instructions on how to run the analyses. References Software GUI: Xu, H., Blonder, B., Jodra, M., Malhi, Y. and Fricker, M.D. (2020) Automated and accurate segmentation of leaf venation networks via deep learning. New Phytol. (In press). Analysis of trait data: Blonder, B., S. Both, M. Jodra, H. Xu, M. Fricker, I. S. Matos, N. Majalap, D. F. R. P. Burslem, Y. Teh and Y. Malhi (2020) Linking functional traits to multiscale statistics of leaf venation networks. New Phytol. (In press). Original image data set and ground truths Blonder, B., Both, S., Jodra, M., Majalap, N., Burslem, D., Teh, Y. A., and Malhi, Y. (2019) Leaf venation networks of Bornean trees: images and hand-traced segmentations. Ecology 100: e02844.10.1002/ecy.2844. Available from: https://ora.ox.ac.uk/objects/uuid:de65fc07-4b8f-4277-a6c4-82836afbdeb3 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4008613 |
| Title | Leaf Vein Network CNN Images |
| Description | This download site contains the CNN vein network predictions and set of Matlab programs that were used for the analyses in Xu et al., (2020) and Blonder et al., (2020). These require Matlab 2020a or later. They may work on earlier versions of MatLab, but this has not been tested and cannot be guaranteed. The files are as follows: Zip files (e.g. BEL_downsampled_images.zip) containing a complete set of images of leaf vein predictions from a fully trained convolutional neural network (CNN), along with the ground truth data. Each folder in the unzipped file contains a sample represented by a CODE with format X-TY-BZ. X represents the name of a plot in the Global Ecosystems Monitoring network database (e.g. 'BEL'). Tree (T) Y indicates the number of a tree within a plot (e.g. '101') and Z represents the light stratum of the canopy where the leaf was collected (either 'S' for 'sunlit' or 'SH' for 'shaded'). A set of Matlab programs (Matlab files.zip) to compare the CNN predictions against other vein extraction approaches. A Matlab Readme file with instructions on how to run the analyses. References Software GUI: Xu, H., Blonder, B., Jodra, M., Malhi, Y. and Fricker, M.D. (2020) Automated and accurate segmentation of leaf venation networks via deep learning. New Phytol. (In press). Analysis of trait data: Blonder, B., S. Both, M. Jodra, H. Xu, M. Fricker, I. S. Matos, N. Majalap, D. F. R. P. Burslem, Y. Teh and Y. Malhi (2020) Linking functional traits to multiscale statistics of leaf venation networks. New Phytol. (In press). Original image data set and ground truths Blonder, B., Both, S., Jodra, M., Majalap, N., Burslem, D., Teh, Y. A., and Malhi, Y. (2019) Leaf venation networks of Bornean trees: images and hand-traced segmentations. Ecology 100: e02844.10.1002/ecy.2844. Available from: https://ora.ox.ac.uk/objects/uuid:de65fc07-4b8f-4277-a6c4-82836afbdeb3 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4008614 |
| Title | Leaf Vein Network CNN Results |
| Description | Results for leaf vein networks extracted using the LeafVeinCNN software package. The original image data set is available from Blonder et al. (2019) https://doi.org/10.1002/ecy.2844. The LeafVeinCNN software used in the analysis is available at https://doi.org/10.5281/zenodo.4007731. The Results_xxx.zip files contain all the Excel results spreadsheets separated by the code for each field site. results.xls provides a summary of all the network metrics for each file that was analysable Results_figures.pdf provides a summary image of the processing steps and results for each leaf segment Network_images.pdf contains a colour-coded image of each network superimposed on the leaf segment HLD_plots shows the binary tree following Hierarchical Network Decomposition PR_results.zip contains the Excel spreadsheets for evaluation of different enhancement methods for each leaf segment. PR_summary.xls provides a summary of the performance of each enhancement method. PR_F1_images.pdf and PR_FBeta2_images.pdf show the pixel classification for each enhancement and segmentation method compared to the manual ground-truth using two different optimum criteria (F1 and FBeta2). PR_fullwidth_plots show the full Precision-Recall plots for the full-width binary image compared to the manual ground-truth using the FBeta2 metric. PR_skeleton_plots show the full Precision-Recall plots for the skeletonised binary image compared to the manual ground-truth using the FBeta2 metric. PR_threshold_plots.pdf show how a set of network metrics vary with the segmentation threshold for each enhancement method. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4008360 |
| Title | Leaf Vein Network CNN Results |
| Description | Results for leaf vein networks extracted using the LeafVeinCNN software package. The original image data set is available from Blonder et al. (2019) https://doi.org/10.1002/ecy.2844. The LeafVeinCNN software used in the analysis is available at https://doi.org/10.5281/zenodo.4007731. The Results_xxx.zip files contain all the Excel results spreadsheets separated by the code for each field site. results.xls provides a summary of all the network metrics for each file that was analysable Results_figures.pdf provides a summary image of the processing steps and results for each leaf segment Network_images.pdf contains a colour-coded image of each network superimposed on the leaf segment HLD_plots shows the binary tree following Hierarchical Network Decomposition PR_results.zip contains the Excel spreadsheets for evaluation of different enhancement methods for each leaf segment. PR_summary.xls provides a summary of the performance of each enhancement method. PR_F1_images.pdf and PR_FBeta2_images.pdf show the pixel classification for each enhancement and segmentation method compared to the manual ground-truth using two different optimum criteria (F1 and FBeta2). PR_fullwidth_plots show the full Precision-Recall plots for the full-width binary image compared to the manual ground-truth using the FBeta2 metric. PR_skeleton_plots show the full Precision-Recall plots for the skeletonised binary image compared to the manual ground-truth using the FBeta2 metric. PR_threshold_plots.pdf show how a set of network metrics vary with the segmentation threshold for each enhancement method. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4008361 |
| Title | Stark et al traits |
| Description | Measurements of functional traits and environment in Colorado alpine plant communities |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Supported one publication in Oikos |
| Title | Venation |
| Description | Images of leaf venation networks for 150 Peruvian, 150 Bornean, and soon 100 Gabonese tree species |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Analyses of these images has supported two manuscripts focused on linking traits to environment, and will be usable for future synthetic work. |
| URL | http://clearedleaves-db.org |
| Description | BALI |
| Organisation | University of Aberdeen |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration on fieldwork in Malaysian Borneo for trait-based analyses |
| Collaborator Contribution | Collaboration on fieldwork in Malaysian Borneo for trait-based analyses; research permit facilitation |
| Impact | Image analysis methods paper in preparation; large image dataset (700+ Bornean leaf vein images) in preparation for Data Dryad; ecological paper synthesizing findings in preparation. |
| Start Year | 2015 |
| Description | BALI |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration on fieldwork in Malaysian Borneo for trait-based analyses |
| Collaborator Contribution | Collaboration on fieldwork in Malaysian Borneo for trait-based analyses; research permit facilitation |
| Impact | Image analysis methods paper in preparation; large image dataset (700+ Bornean leaf vein images) in preparation for Data Dryad; ecological paper synthesizing findings in preparation. |
| Start Year | 2015 |
| Description | CTEMPS |
| Organisation | Oregon State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Drone-based remote sensing work on forest structure in Colorado |
| Collaborator Contribution | Collaborators flew 5-band multispectral drone over several research sites in Colorado and provided image datasets for later analysis to our team. |
| Impact | Data still being analyzed |
| Start Year | 2017 |
| Description | Jessica Blois |
| Organisation | University of California, Merced |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Analysis of paleoecological datasets related to pollen assemblages in North America |
| Collaborator Contribution | Contribution of paleoecological datasets and expertise |
| Impact | 2017 paper in Ecology Letters - also co-supervision of masters student with manuscript in review at Ecography |
| Start Year | 2016 |
| Description | Norway |
| Organisation | Norwegian University of Science and Technology (NTNU) |
| Country | Norway |
| Sector | Academic/University |
| PI Contribution | Collaborating on theory development, field measurements in montane systems |
| Collaborator Contribution | Collaborating on theory development; sharing students for fieldwork on alpine systems |
| Impact | Two masters' students supervised; one grant proposal on microclimate; one paper on species coexistence accepted; one paper on community dynamics accepted; one more masters' student supervision in progress |
| Start Year | 2015 |
| Description | Sean Michaletz |
| Organisation | Los Alamos National Laboratory |
| Country | United States |
| Sector | Public |
| PI Contribution | Theory development on plant energy balance; grantwriting. |
| Collaborator Contribution | Theory development on plant energy balance; fieldwork contribution; grantwriting. |
| Impact | Two manuscripts - one in review at Plant Physiology; one in preparation |
| Start Year | 2015 |
| Title | Leaf Vein Network CNN Analysis Software |
| Description | Software to extract and analyse leaf vein networks using convolutional neural networks. LeafVeinCNN.mlappinstall - installs the software and trained CNN models as a matlab app (requires Matlab 2020a or later). Note the Deep Learning Toolbox and Image Processing Toolbox are required. In addition, the support package importKerasNetwork needs to be installed using the Add-On Explorer LeafVeinCNN.exe - installs the software and trained CNN models as a standalone package for Windows 10. This will automatically download the Matlab runtime library from the web during installation. (Jan 2021 - Please note we are aware of installation problems with this release on some systems and are currently working on a workaround). LeafVeinCNN_Manual.pdf - A user manual describing installation and use of the software. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4007731 |
| Title | Leaf Vein Network CNN Analysis Software |
| Description | Software to extract and analyse leaf vein networks using convolutional neural networks. LeafVeinCNN.mlappinstall - installs the software and trained CNN models as a matlab app (requires Matlab 2020a or later). Note the Deep Learning Toolbox and Image Processing Toolbox are required. In addition, the support package importKerasNetwork needs to be installed using the Add-On Explorer LeafVeinCNN.exe - installs the software and trained CNN models as a standalone package for Windows 10. This will automatically download the Matlab runtime library from the web during installation. (Jan 2021 - Please note we are aware of installation problems with this release on some systems and are currently working on a workaround). LeafVeinCNN_Manual.pdf - A user manual describing installation and use of the software. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4007730 |
| Description | Sky School |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Environmental education programs in southern Arizona reached groups of ~10 students for 20 10-hour days per year. Teaching was delivered by a graduate student employed by this grant. These programs lead to more positive attitudes towards science and science careers. |
| Year(s) Of Engagement Activity | 2015,2016,2017 |
| Description | Sky School writing |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Sponsored curriculum development and mentoring of secondary school students on inquiry-based field ecology research projects in desert environments, culminating in annual regional science fair presentations. 67% of participants students won awards in the first pilot year; enrollment doubled in second and third year. |
| Year(s) Of Engagement Activity | 2016,2017 |
| URL | http://skyschool.arizona.edu/research-apprenticeship/ |
| Description | Teacher professional development |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Conducted teacher training workshops with entire class of geography teacher trainees at Oxford, centered around inquiry-based field education. Developed and shared educational materials around open-ended inquiry, provided advice on ways to better integrate these topics into classrooms. |
| Year(s) Of Engagement Activity | 2010,2016,2017 |