CropQuant-Air

Jie Zhou¹, Jiawei Chen¹, Ji Zhou^1,2*

¹State Key Laboratory of Crop Genetics & Germplasm Enhancement, Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China;

²Cambridge Crop Research, National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK.

• JieZhou@njau.edu.cn • Ji.Zhou@njau.edu.cn; Ji.Zhou@NIAB.com

Overview

In this release, we uploaded the latest version of CropQuant-Air, a graphical user interface (GUI, in .exe format) based analytic software that integrate deep learning algorithms and traditional image processing algorithms, directly extract and output yield- and performance-related phenotypic traits, and added the function of batch processing a series of images collected by low-cost drones.

Relevant publications

• CropQuant-Air: an AI-powered system to enable phenotypic analysis of yield- and performance-related traits using wheat canopy imagery collected by low-cost drones (DOI: 10.3389/fpls.2023.1219983) • AirMeasurer: open-source software to quantify static and dynamic traits derived from multiseason aerial phenotyping to empower genetic mapping studies in rice (DOI: 10.1111/nph.18314)

Install Python, Anaconda and Libraries

If you wish to run CropQuant-Air from the code, you will need to set up Python on your system.

1. 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/

   • CropQuant-Air only supports Python 3

2. 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

   • An Anaconda Graphical installer can be found via: https://www.continuum.io/downloads

   • We recommend users install the latest Anaconda Python distribution

3. Install packages:

   • CropQuant-Air uses a number of 3rd-party libraries that you may need to add to your conda environment. These include, but are not limited to:

   Scikit-image=0.20.0
   Opencv-python=4.7.0.72
   Matplotlib =3.7.1
   Pandas=2.0.1
   Numpy=1.24.2
   Scipy=1.9.1
   Torch=1.11.0+cu113
   

Running CropQuant-Air

Before using the software and source code, please see the CropQuant-Air user guide.pdf file on this repository. A compressed Windows (exe format, i.e. CropQuant-Air.zip) file can be downloaded from the release link as well.