Quantification-of-morphology-PhD-project_Method

Code for the quantification of geometry (area & perimeter) and shape (procrustes distance) of single-cell plant structures and its analysis under nitrogen & phosphorus stress compared to the control.

Installation

1. git clone https://github.com/Ankita-30/Quantification-of-morphology-PhD-project_Method.git
2. run ./build.sh , if permission is deined do $ chmod 700 build.sh re-run $ ./build.sh
3. To create the env run $ source hookedHairQuantifucation/bin/activate'
4. Install all dependent requrements by $ pip install -r requirements.txt

Run

Generation

1. To generate individual hooked hair run python3 extractRH.py DataAnalysis/RGB/Control_trial DataAnalysis/RGB python3 extractRH.py input-path output-path Directory folders are local for example, input the data directory on your system

• DataAnalysis/RGB/Control_trial is the input path with segmented microscopic images of hooked hairs
• DataAnalysis/RGB/Control_trial is the output path where extracted individual hooked hairs are saved

Quantification

2. To calculate area and perimeter of extracted hooked hair run python3 Perimeter+CS.py DataAnalysis/RGB DataAnalysis/, 'python3 Perimeter+CS.py input-path output-path' DataAnalysis/RGB should be the output directory from step 1

Analysis

4. To analyze how the area and perimeter of 'hooked' hairs changes under stress for each day (3,4,5) and growth category (low,mid,high) run python3 Data_Analysis_AP.py Data_Files_Morphology/DataCellShapeC_pipeline.csv Data_Files_Morphology/DataCellShapeNS_pipeline.csv Data_Files_Morphology/DataCellShapePS_pipeline.csv output-path

5. To analyze how length of 'hooked' hairs changes under stress for each day (3,4,5) and growth category (low,mid,high) run python3 Data_Analysis_Length.py Data_Files_Morphology/Data_cellshapeC_length.csv Data_Files_Morphology/Data_cellshapePS_length.csv Data_Files_Morphology/Data_cellshapeNS_length.csv output-path

6. To analyze how shape of 'hooked' hairs changes under stress for each day (3,4,5) and growth category (low,mid,high)run python3 Data_Analysis_Shape_PD.py Data_Files_Morphology/Data_cellshape_Control.csv Data_Files_Morphology/Data_cellshape_PStress.csv Data_Files_Morphology/Data_cellshape_NStress.csv output-path

'python3 Data_Analysis_AP.py/Data_Analysis_Shape_PD.py input-path1 input-path2 input-path3 output-path' input path 1,2 & 3 are the output paths from step 3 & step 4 respectively for the 3 treatment conditions (Control(C), P-stress(PS) & N-stress(NS)) specific to our experiment output-path is the location to store the output csv file

7. To analyze how the area & perimeter of'hooked hairs' change with age and growth of the plant in early development run python3 violinplot_statistics_AP.py Data_Files_Morphology/DataCellShapeC_pipeline.csv Data_Files_Morphology/DataCellShapeNS_pipeline.csv Data_Files_Morphology/DataCellShapePS_pipeline.csv

8. To analyze how the length of'hooked hairs' changes with age and growth of the plant in early development run python3 violinplot_statistics_Length.py Data_Files_Morphology/Data_cellshapeC_length.csv Data_Files_Morphology/Data_cellshapePS_length.csv Data_Files_Morphology/Data_cellshapeNS_length.csv

9. To analyze how the shape of'hooked hairs' changes with age and growth of the plant in early development run python3 violinplot_statistics_shape_PD.py Data_Files_Morphology/Data_cellshape_Control.csv Data_Files_Morphology/Data_cellshape_PStress.csv Data_Files_Morphology/Data_cellshape_NStress.csv

'python3 Data_Analysis_AP.py/Data_Analysis_Shape_PD.py input-path1 input-path2 input-path3' input path 1,2 & 3 are the same input files used in step 4,5 & 6 respectively.

Hooking Axis Histogram

1. To plot the histogram representing the degree of hooking in a curled root hair image run python3 curledroothairaxis.py Hooking_images/curledroothair_commonbean.png
2. To plot the histogram representing the degree of hooking in a hooked hair image run python3 hookedhairaxis.py Hooking_images/hookedhair_commonbean.png
3. To plot the histogram representing the degree of hooking in a trichome image run python3 hookedhairaxis.py Hooking_images/trichome_commonbean.png