Update to readme, pyproject.toml, citation, disclaimer, and license file

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

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

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.

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.

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"