Dr. Kefauver while at the Integrative Crop Ecophysiology Group at the Universitat de Barecelona and Agrotecnio has developed ten open-source image processing tools in the past 10 years, including 4 software plugins, 3 mobile apps and 3 standalone JAVA apps, which can be found on our gits and websites: https://github.com/doctorxub/.github, https://integrativecropecophysiology.com/software-development/, https://github.com/sckefauver/, and https://gitlab.com/sckefauver.
Advanced analyses for hyperspectral data, created as part of the PANGEOS COST Action network are at https://github.com/pangeos-cost.
A. Open-Source Plugins for FIJI (Image J free image processing software platform) Software Development.
1. CIMMYT MaizeScanner (https://github.com/sckefauver/CIMMYT, open access, open-source, copyright Shawn Carlisle Kefauver 2015): FIJI plugin that provides image analyses for RGB image processing with general crop assessments and specific machine learning algorithms for scoring Maize Lethal Necrosis impacts.
2. CerealScanner (https://gitlab.com/sckefauver/cerealscanner, copyright Shawn Carlisle Kefauver 2018): FIJI plugin with a suite of field phenotyping tools for cereal breeding including general crop vigor and calculations for specific traits early vigor fractional area cover/biomass, wheat and barley ear counting, and senescence.
3. MosaicTool (https://gitlab.com/sckefauver/MosaicTool, copyright Shawn Carlisle Kefauver 2018): FIJI plugin for semi-automated data extraction to the plot level and data processing for producing vegetation indices for crop phenotyping from RGB, VNIR multispectral and TIR image data from UAV-based image mosaics.
4. ForestScanner (https://github.com/sckefauver/QualityPinea, copyright Shawn Carlisle Kefauver 2022): FIJI plugin that provide support forest tree level for producing vegetation indices for forestry management from RGB, VNIR multispectral and 3D digital elevation or digital vegetation models.
B. Mobile phone app developments in web-apps and for Android:
5. Doctor X Nabat, copyright Shawn Carlisle Kefauver 2022, online web app (https://doctorxub.com/icba) and in Android on Google Play (https://play.google.com/store/apps/details?id=com.doctorxnabat). Artificial intelligence deep learning algorithms to identify common pests and for cucumber, tomatoes, pepper, and quinoa for supporting sustainable agricultural management in N. Africa and the Middle East.
6. Doctor X CTFC, copyright Shawn C. Kefauver 2021, online web app (https://ctfc.doctorxub.com/) for the automatic counting of pinecones from UAV images. Developed in collaboration with the Catalan Technologic Forest Center (CTFC) and the University of Ibague, Tolima, Colombia.
7. Hue Enhanced Agricultural Temperature (H.E.A.T.) (https://gitlab.com/sckefauver/heat, copyright Shawn Carlisle Kefauver 2018): Mobile phone app including Hue Enhanced Agricultural Temperature (HEAT) RGB+TIR fusion algorithms for thermal imaging with CAT S60 android mobile phone device.
C. Standalone JAVA-based automated PC-based processing tools connected to Open Data Kit, ODK.
8. BreedpixFusion (https://gitlab.com/sckefauver/fusion, copyright Dr. Kefauver 2018): JAVA-based automated PC-based processing tool for crop phenotyping image data collected with a mobile phone as part of an Open Data Kit (odk.org) android application formula.
9. CerealsFusion https://gitlab.com/sckefauver/cerealfusion, copyright Dr. Kefauver 2018): JAVA PC-based processing tool for field phenotyping tools for cereal breeding including crop vigor and early vigor fractional area cover/biomass, wheat and barley ear counting, and crop senescence using Open Data Kit (odk.org) forms.
10. ODK Downloader (https://gitlab.com/sckefauver/odk-downloader, Beta, open access, under development, copyright Dr. Kefauver 2024): JAVA-based automated tool for downloading ODK developed mobile phone image databases for the AI development on Google Collab.
Shawn C. Kefauver 