Releases: The-Zhou-Lab/LiDAR
Publication Release
Overview
In this release, we uploaded the latest version of CropQuant-3D, a graphical user interface (GUI, in .exe format) based analytic software that can be utilised to carry out 3D trait analysis on LiDAR-collected point cloud data in large-scale field phenotyping. The use of backpack LiDAR or other sources can acquire millions of 3D points to represent spatial features of crops. To effectively analyse these point clouds, CropQuant-3D was developed to extract plot-based phenotypic traits from large, complex point clouds with limited computing time and power. We combined a backpack LiDAR device and CropQuant-3D to quantify crop height, 3D canopy index (3DCI, an original 3D measurement of canopy variation), 3D canopy surface, canopy coverage and biomass estimation (i.e. 3DVI and 3DPI), in a case study examining the response of wheat varieties to three different levels of nitrogen fertilisation in field experiments. The combined solution can differentiate significant genotype and treatment effects on key performance-related morphological traits and structural variation in canopy, with strong correlations with conventional manual measurements. Hence, we believe that CropQuant-3D could be used for consistently quantifying key traits at a larger scale and more quickly than heretofore possible, which could be used as a reliable research tool and jointly developed with the plant research community for large-scale and multi-location field phenotyping in crop research and breeding activities.
License of CropQuant-3D
The CropQuant-3D software and its analysis algorithms are released under the
following license (MIT License):
Copyright 2021, The Zhou Laboratory, at the Nanjing Agricultural University, Nanjing China, as well as the Cambridge Crop Research, National Institute of Agricultural Botany, Cambridge UK
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 NON-INFRINGEMENT. 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.
Packaged third party libraries are distributed with licenses as stated on their associated websites.
Publication Release
Overview
In this release, we uploaded the latest version of CropQuant-3D, a graphical user interface (GUI, in .exe format) based analytic software that can be utilised to carry out 3D trait analysis on LiDAR-collected point cloud data in large-scale field phenotyping. The use of backpack LiDAR or other sources can acquire millions of 3D points to represent spatial features of crops. To effectively analyse these point clouds, CropQuant-3D was developed to extract plot-based phenotypic traits from large, complex point clouds with limited computing time and power. We combined a backpack LiDAR device and CropQuant-3D to quantify crop height, 3D canopy index (3DCI, an original 3D measurement of canopy variation), 3D canopy surface, canopy coverage and biomass estimation (i.e. 3DVI and 3DPI), in a case study examining the response of wheat varieties to three different levels of nitrogen fertilisation in field experiments. The combined solution can differentiate significant genotype and treatment effects on key performance-related morphological traits and structural variation in canopy, with strong correlations with conventional manual measurements. Hence, we believe that CropQuant-3D could be used for consistently quantifying key traits at a larger scale and more quickly than heretofore possible, which could be used as a reliable research tool and jointly developed with the plant research community for large-scale and multi-location field phenotyping in crop research and breeding activities.
License of CropQuant-3D
The CropQuant-3D software and its analysis algorithms are released under the
following license (MIT License):
Copyright 2021, The Zhou Laboratory, at the Nanjing Agricultural University, Nanjing China, as well as the Cambridge Crop Research, National Institute of Agricultural Botany, Cambridge UK
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 NON-INFRINGEMENT. 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.
Packaged third party libraries are distributed with licenses as stated on their associated websites.
Publication Release
The CropQuant-3D software and its analysis algorithms are released under the
following license (MIT License):
Copyright 2021, The Zhou Laboratory, at the Nanjing Agricultural University, Nanjing
China, as well as the Cambridge Crop Research, National Institute of Agricultural
Botany, Cambridge UK
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.
Packaged third party libraries are distributed with licenses as stated on their
associated websites.
Publication Release
CropQuant-3D
Yulei Zhu1, Gang Sun1, Jie Zhou1, Ji Zhou1,2*
11State Key Laboratory of Crop Genetics & Germplasm Enhancement, Plant Phenomics Research Center, College of Engineering, Jiangsu Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
2Cambridge Crop Research, National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK
*Correspondence: Ji.Zhou@NJAU.edu.cn or Ji.Zhou@NIAB.com
Install Python, Anaconda and Libraries
If you wish to run CropQuant-3D from the code, you will need to set up Python on your system.
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Install Python releases:
• Read the beginner’s guide to Python if you are new to the language:
https://wiki.python.org/moin/BeginnersGuide• For Windows users, Python 3 release can be downloaded via:
https://www.python.org/downloads/windows/• For Mac OS users, Python 3 release can be downloaded via:
https://www.python.org/downloads/mac-osx/• CropQuant-3D only supports Python 3 onwards
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Install Anaconda Python distribution:
• Read the install instruction using the URL: https://docs.continuum.io/anaconda/install
• For Windows users, a detailed step-by-step installation guide can be found via:
https://docs.continuum.io/anaconda/install/windows• For Mac OS users, a detailed step-by-step installation guide can be found via:
https://docs.continuum.io/anaconda/install/mac-os.html• An Anaconda Graphical installer can be found via:
https://www.continuum.io/downloads• We recommend users install the latest Anaconda Python distribution
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Install packages:
• CropQuant-3D uses a number of 3rd-party libraries that you may need to add to your conda environment.
These include, but are not limited to:Laspy=1.7.0 Whitebox==1.3.0 GDAL=3.1.4 Rasterio=1.1.8 Open3d==0.11.2 mayavi==4.7.2 Scikit-image=0.17.2 Opencv-python==4.4.0.46 Matplotlib =3.3.3 Pandas=1.1.5 Numpy=1.19.4 Scipy=1.5.3
Running CropQuant-3D
Please see the README.doc file that is included in this repository.
We have a Windows .exe file (CropQuant-3D-1.0.zip) you can download.