Morley: Image Analysis and Evaluation of Statistically Significant Differences in Geometric Sizes of Crop Seedlings in Response to Biotic Stimulation

Round 1

Reviewer 1 Report

This paper introduces Morley, an open source graphical user interface tool for automatic analysis and processing of large group plant images. The tool has the functions of population analysis, seed, seedling and root identification, calculation of length, area, shape and other parameters, evaluation of statistically significant differences between plant populations, calculation of germination rate, visualization and interpretation. The analysis method of corn seedling growth with this tool was also introduced. Considering delayed germination seeds, the Scipy.stats library was used for statistical evaluation, and Unpaired T-test or Mann-Whitney test was used to compare the two groups of samples.

 

This paper provides an effective plant image analysis tool, which can greatly reduce the workload of laboratory analysis and data processing, and improve the efficiency and accuracy of analysis. The tool is suitable for laboratory research and development of new bioactive chemicals, fertilizers and crop varieties, and analysis at an early stage to provide more accurate results for greenhouse and field trials.

 

In summary, this paper introduces a practical, free and open source graphical user interface tool, which can be effectively used to automatically analyze and process images of large groups of plants and calculate related parameters. This tool has a good application prospect and is worthy of further promotion and use.

Author Response

Response to Reviewer 1 Comments

Point 1. This paper introduces Morley, an open source graphical user interface tool for automatic analysis and processing of large group plant images. The tool has the functions of population analysis, seed, seedling and root identification, calculation of length, area, shape and other parameters, evaluation of statistically significant differences between plant populations, calculation of germination rate, visualization and interpretation. The analysis method of corn seedling growth with this tool was also introduced. Considering delayed germination seeds, the Scipy.stats library was used for statistical evaluation, and Unpaired T-test or Mann-Whitney test was used to compare the two groups of samples.

This paper provides an effective plant image analysis tool, which can greatly reduce the workload of laboratory analysis and data processing, and improve the efficiency and accuracy of analysis. The tool is suitable for laboratory research and development of new bioactive chemicals, fertilizers and crop varieties, and analysis at an early stage to provide more accurate results for greenhouse and field trials.

In summary, this paper introduces a practical, free and open source graphical user interface tool, which can be effectively used to automatically analyze and process images of large groups of plants and calculate related parameters. This tool has a good application prospect and is worthy of further promotion and use.

RESPONSE 1: Thank you very much for the positive response. We will be happy if you find our tool useful for your work and we are ready to support your experience with Morley.

Reviewer 2 Report

This manuscript (agronomy-2530911) introduces Morley, a Python-based open-source tool that streamlines the image analysis and statistical evaluation of seedling growth for numerous plants. The software enhances research by automating seedling identification, measuring morphometrics, calculating germination rates, and evaluating significant differences between plant groups, with its accuracy validated on T. aestivum and P. sativum cultivars.

The article is interesting; however, some sections need to be reviewed and rewritten before the work can be accepted.

The tables and figures are of good quality, as are the captions. Small corrections are necessary.

Please, check all the standardisation in the manuscript according to the authors' instructions.

Keywords in alphabetic order;

Please, what is the hypothesis of your work? It is not clear at the end of the introduction. Make your objectives clear as well.

The 'Materials and Methods' section should be checked. For example, it does not start with 'Table 1'. Talk about the different experiments, the species used, and provide the necessary context. What were the appropriate growth conditions?

Please, check the scientific notations and molecular representations throughout the manuscript.

some citations are incorrect, for example at line 225.

The discussion in the manuscript is not adequate. It needs to explain the results and compare them with other data and previously published work. Furthermore, there are no references in this section. Finally, consider adding a conclusion section emphasising the key findings of your work and outlining future perspectives.

Check old references;

Check grammar and spelling;

Author Response

Response to Reviewer 2 Comments

Point 1. This manuscript (agronomy-2530911) introduces Morley, a Python-based open-source tool that streamlines the image analysis and statistical evaluation of seedling growth for numerous plants. The software enhances research by automating seedling identification, measuring morphometrics, calculating germination rates, and evaluating significant differences between plant groups, with its accuracy validated on T. aestivum and P. sativum cultivars.

The article is interesting; however, some sections need to be reviewed and rewritten before the work can be accepted.

The tables and figures are of good quality, as are the captions. Small corrections are necessary.

Please, check all the standardisation in the manuscript according to the authors' instructions.

Keywords in alphabetic order;

RESPONSE 1: Thank you very much for your response. We checked and corrected formatting of tables, figures, legends and text throughout the manuscript according to the author’s instructions. Also we corrected the order of keywords.

Point 2. Please, what is the hypothesis of your work? It is not clear at the end of the introduction. Make your objectives clear as well.

RESPONSE 2: We revised the end of the introduction to clarify the hypothesis of the work and our objectives.

Point 3. The 'Materials and Methods' section should be checked. For example, it does not start with 'Table 1'. Talk about the different experiments, the species used, and provide the necessary context. What were the appropriate growth conditions?

RESPONSE 3: We checked and corrected the Materials and Methods section. The 2.1. Seeds paragraph contains information about where and what seeds were purchased, country of origin, for which experiments they were used and the number of biological replicates. This information is summarized in Table 1. The 2.2 and 2.3 paragraphs clarify growth and treatment conditions, respectively.

Point 4. Please, check the scientific notations and molecular representations throughout the manuscript.

some citations are incorrect, for example at line 225.

RESPONSE 4: We checked and corrected all citations throughout the manuscript. Тhe ImageJ software is cited according to the recommendation of their developers: Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671–675. doi:10.1038/nmeth.2089.

Point 5. The discussion in the manuscript is not adequate. It needs to explain the results and compare them with other data and previously published work. Furthermore, there are no references in this section. Finally, consider adding a conclusion section emphasising the key findings of your work and outlining future perspectives.

RESPONSE 5: Agree. Discussion was extensively revised to meet the comments. We discussed the results comparing them with other published studies and added appropriate references. We also added the Conclusions section to emphasize the key points of our work and outline future perspectives.

Point 6. Check old references;

RESPONSE 6: We checked and corrected all citations throughout the manuscript. 

Point 7. Comments on the Quality of English Language  -   Check grammar and spelling;

RESPONSE 7: Corrected.

Reviewer 3 Report

In the manuscript the authors underlined the need of a software aimed to automate the estimation of germination rates and statistically significant morphometric changes induced by treatments with biochemical agents. For this reason, they developed Morley, an open source tool with graphical user interface, providing measures of shoot and root lengths as well as surface areas, germination rates and an interpretation of the related changes.

The performance of the software was also tested and the results showed that the accuracy of the measured morphometric parameters was comparable with the ones obtained using ImageJ and manual measurements. According to these results, Morley, which still needs further testing activities, seems to have the potential to be used in agriculture laboratories.

The software is well documented and external links allowed to access to the documentation which describe it. Testing results are detailed and properly described as well.

However, a better description of the interpretation of the observed changes is suggested.

 Minor editing of English language required

Author Response

Response to Reviewer 3 Comments

Point 1. In the manuscript the authors underlined the need of a software aimed to automate the estimation of germination rates and statistically significant morphometric changes induced by treatments with biochemical agents. For this reason, they developed Morley, an open source tool with graphical user interface, providing measures of shoot and root lengths as well as surface areas, germination rates and an interpretation of the related changes.

The performance of the software was also tested and the results showed that the accuracy of the measured morphometric parameters was comparable with the ones obtained using ImageJ and manual measurements. According to these results, Morley, which still needs further testing activities, seems to have the potential to be used in agriculture laboratories.

The software is well documented and external links allowed to access to the documentation which describe it. Testing results are detailed and properly described as well.

However, a better description of the interpretation of the observed changes is suggested.

RESPONSE 1: Thank you very much for your response. We revised the Discussion section to provide better interpretation of the results obtained in the study. Also, we added the detailed description of all results reported by Morley to the README file (https://github.com/dashabezik/Morley/). We believe it will help users to interpret the results and the observed changes.

Point 2. Comments on the Quality of English Language - Minor editing of English language required

RESPONSE 2: Corrected.