diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..6c9775a --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,133 @@ +cff-version: "1.2.0" +title: "RhizoAI: AI-ready datasets and workflows for rhizosphere imaging and root + classification" +message: "If you use this software or dataset, please cite the associated article." +authors: +- family-names: Hassan + given-names: Mohamed O. + affiliation: "Department of Civil and Environmental Engineering, Texas A&M University, + College Station, TX 77843, USA" + orcid: "https://orcid.org/0009-0007-9006-978X" +- family-names: Truong + given-names: Aramy + orcid: "https://orcid.org/0009-0002-7467-7957" + affiliation: "Environmental Molecular Sciences Laboratory, Pacific Northwest National + Laboratory, Richland, WA 99352, USA" +- family-names: Mudunuru + given-names: Maruti K. + orcid: "https://orcid.org/0000-0002-2158-7723" + affiliation: "Subsurface Science Group, Pacific Northwest National Laboratory, Richland, + WA 99352, USA" + email: maruti@pnnl.gov +- family-names: Butler + given-names: Leslie G. + orcid: "https://orcid.org/0000-0003-1547-608X" + affiliation: "Department of Chemistry, Louisiana State University, Baton Rouge, + LA 70803, USA" +- family-names: Rovai + given-names: Andre + orcid: "https://orcid.org/0000-0003-4117-2055" + affiliation: "Smithsonian Environmental Research Center, Smithsonian Institution, + Edgewater, MD 21037, USA" +- family-names: Vargas-Lopez + given-names: Ivan + orcid: "https://orcid.org/0000-0001-9435-8430" + affiliation: "Department of Oceanography and Coastal Sciences, Louisiana State University, + Baton Rouge, LA 70803, USA" +- family-names: Larimer + given-names: Curtis + orcid: "https://orcid.org/0000-0001-6634-5384" + affiliation: "Chemical and Biological Signatures Group, Pacific Northwest National + Laboratory, Richland, WA 99352, USA" +- family-names: Hermanson + given-names: Clare + affiliation: "Department of Chemistry, University of Colorado Boulder, Boulder, + Colorado 80309" +- family-names: Daddona + given-names: Joseph + affiliation: "Department of Chemistry, University of Oregon, Eugene, Oregon 97403" +- family-names: Ahkami + given-names: Amir H. + orcid: "https://orcid.org/0000-0002-0545-1236" + affiliation: "Environmental Molecular Sciences Laboratory, Pacific Northwest National + Laboratory, Richland, WA 99352, USA" +- family-names: Bardhan + given-names: Jay + orcid: "https://orcid.org/0000-0002-6051-8499" + affiliation: "Environmental Molecular Sciences Laboratory, Pacific Northwest National + Laboratory, Richland, WA 99352, USA" +- family-names: Varga + given-names: Tamas + orcid: "https://orcid.org/0000-0002-5492-866X" + affiliation: "Environmental Molecular Sciences Laboratory, Pacific Northwest National + Laboratory, Richland, WA 99352, USA" +- family-names: Stratton + given-names: Kelly + orcid: "https://orcid.org/0000-0002-1721-9688" + affiliation: "Environmental Molecular Sciences Laboratory, Pacific Northwest National + Laboratory, Richland, WA 99352, USA" +- family-names: Karra + given-names: Satish + orcid: "https://orcid.org/0000-0001-7847-6293" + affiliation: "Environmental Molecular Sciences Laboratory, Pacific Northwest National + Laboratory, Richland, WA 99352, USA" +- family-names: Twilley + given-names: Robert + orcid: "https://orcid.org/0000-0002-6173-6033" + affiliation: "Department of Oceanography and Coastal Sciences, Louisiana State University, + Baton Rouge, LA 70803, USA" +- family-names: Jafari + given-names: Navid H. + orcid: "https://orcid.org/0000-0002-4394-3776" + affiliation: "Department of Civil and Environmental Engineering, Texas A&M University, + College Station, TX 77843, USA" +contact: +- family-names: Mudunuru + given-names: Maruti K. + orcid: "https://orcid.org/0000-0002-2158-7723" + email: maruti@pnnl.gov +preferred-citation: + authors: + - family-names: Hassan + given-names: Mohamed O. + - family-names: Truong + given-names: Aramy + - family-names: Mudunuru + given-names: Maruti K. + - family-names: Butler + given-names: Leslie G. + - family-names: Rovai + given-names: Andre + - family-names: Vargas-Lopez + given-names: Ivan + - family-names: Larimer + given-names: Curtis + - family-names: Hermanson + given-names: Clare + - family-names: Daddona + given-names: Joseph + - family-names: Ahkami + given-names: Amir H. + - family-names: Bardhan + given-names: Jay + - family-names: Varga + given-names: Tamas + - family-names: Stratton + given-names: Kelly + - family-names: Karra + given-names: Satish + - family-names: Twilley + given-names: Robert + - family-names: Jafari + given-names: Navid H. + date-published: 2025-10-15 + doi: 10.1016/j.scitotenv.2025.180315 + journal: "Science of The Total Environment" + publisher: + name: Elsevier + start: 180315 + title: "From pixels to patterns: Coupling Optical Coherence Tomography and machine + learning for monitoring coastal wetland root systems" + type: article + url: "https://doi.org/10.1016/j.scitotenv.2025.180315" + volume: 999 diff --git a/DISCLAIMER.md b/DISCLAIMER.md new file mode 100644 index 0000000..797875b --- /dev/null +++ b/DISCLAIMER.md @@ -0,0 +1,24 @@ +DISCLAIMER + +This material was prepared as an account of work sponsored by an agency of the +United States Government. Neither the United States Government nor the United +States Department of Energy, nor Battelle, nor any of their employees, nor any +jurisdiction or organization that has cooperated in the development of these +materials, makes any warranty, express or implied, or assumes any legal +liability or responsibility for the accuracy, completeness, or usefulness or +any information, apparatus, product, software, or process disclosed, or +represents that its use would not infringe privately owned rights. + +Reference herein to any specific commercial product, process, or service by +trade name, trademark, manufacturer, or otherwise does not necessarily +constitute or imply its endorsement, recommendation, or favoring by the United +States Government or any agency thereof, or Battelle Memorial Institute. The +views and opinions of authors expressed herein do not necessarily state or +reflect those of the United States Government or any agency thereof. + + PACIFIC NORTHWEST NATIONAL LABORATORY + operated by + BATTELLE + for the + UNITED STATES DEPARTMENT OF ENERGY + under Contract DE-AC05-76RL01830 diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..f7046a4 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2026 Pacific Northwest National Laboratory + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. \ No newline at end of file diff --git a/README.md b/README.md index 3587661..0176238 100644 --- a/README.md +++ b/README.md @@ -43,57 +43,10 @@ pip install ".[method2]" 1. **Preprocessing**: Use the `preprocess.py` module to preprocess the OCT images and prepare the data for classification. 2. **Feature Extraction**: Utilize the `feature_extraction.py` module to extract features from the images. 3. **Model Training**: - - For Method 1, run the `method1_classifier.py` to train the Random Forest model using flattened data data. + - For Method 1, run the `method1_classifier.py` to train the Random Forest model using flattened data. - For Method 2, run the `method2_classifier.py` to train the model using HOG features extracted from the images. 4. **Evaluation**: Evaluate the model performance using the provided Jupyter Notebooks. ## Contributing Contributions are welcome! Please open an issue or submit a pull request for any improvements or bug fixes. -## License and Disclaimer -DISCLAIMER: - -This material was prepared as an account of work sponsored by an agency of the -United States Government. Neither the United States Government nor the United -States Department of Energy, nor Battelle, nor any of their employees, nor any -jurisdiction or organization that has cooperated in the development of these -materials, makes any warranty, express or implied, or assumes any legal -liability or responsibility for the accuracy, completeness, or usefulness or -any information, apparatus, product, software, or process disclosed, or -represents that its use would not infringe privately owned rights. - -Reference herein to any specific commercial product, process, or service by -trade name, trademark, manufacturer, or otherwise does not necessarily -constitute or imply its endorsement, recommendation, or favoring by the United -States Government or any agency thereof, or Battelle Memorial Institute. The -views and opinions of authors expressed herein do not necessarily state or -reflect those of the United States Government or any agency thereof. - - PACIFIC NORTHWEST NATIONAL LABORATORY - operated by - BATTELLE - for the - UNITED STATES DEPARTMENT OF ENERGY - under Contract DE-AC05-76RL01830 - -LICENSE: - -Copyright Battelle Memorial Institute 2026 - -Permission is hereby granted, free of charge, to any person obtaining a copy of -this software and associated documentation files (the "Software"), to deal in -the Software without restriction, including without limitation the rights to -use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies -of the Software, and to permit persons to whom the Software is furnished to do -so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/pyproject.toml b/pyproject.toml index 1375f2e..600ab22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,22 +6,22 @@ build-backend = "setuptools.build_meta" name = "rhizoai" version = "0.0.1" authors = [ - { name="Mohamed Hassan", email="mhassan@tamu.edu" }, + { name="Mohamed O. Hassan", email="mhassan@tamu.edu" }, { name="Aramy Truong", email="aramy.truong@pnnl.gov" }, - { name="Maruti Mudunuru", email="maruti@pnnl.gov" }, - { name="Leslie Butler"}, - { name="Andre Rovai"}, - { name="Ivan Vargas-Lopez"}, - { name="Curtis Larimer"}, - { name="Claire Hermanson"}, - { name="Joseph Daddona"}, - { name="Amir Ahkami"}, - { name="Jay Bardhan"}, - { name="Tamas Varga", email="tamas.varga@pnnl.gov" }, - { name="Kelly Stratton"}, + { name="Maruti K. Mudunuru", email="maruti@pnnl.gov" }, + { name="Leslie G. Butler", email="lbutler@lsu.edu" }, + { name="Andre Rovai", email="rovaias@si.edu" }, + { name="Ivan Vargas-Lopez", email="ivarga2@lsu.edu" }, + { name="Curtis Larimer", email="curtis.larimer@pnnl.gov" }, + { name="Clare Hermanson", email="Clare.Hermanson@colorado.edu" }, + { name="Joseph Daddona", email="jdaddona@uoregon.edu" }, + { name="Amir H. Ahkami", email="amir.ahkami@pnnl.gov" }, + { name="Jay Bardhan", email="jaydeep.bardhan@pnnl.gov" }, + { name="Tamas Varga", email="Tamas.Varga@pnnl.gov" }, + { name="Kelly Stratton", email="kelly.stratton@pnnl.gov" }, { name="Satish Karra", email="karra@pnnl.gov" }, - { name="Robert Twilley"}, - { name="Navid Jafari"}, + { name="Robert Twilley", email="rtwilley@lsu.edu" }, + { name="Navid H. Jafari", email="njafari@tamu.edu" }, ] description = "A package to preprocess AI-ready datasets for rhizosphere imaging and root classification" readme = "README.md"