Update DataGuide_AAPF_HSI.md

DataGuide_AAPF_HSI.md

@@ -10,41 +10,41 @@ This document details the file system organization and navigation procedures for
 ### File system structure
 
 
-#### Raw Scanned Data
+    #### Raw Scanned Data
 
-Directories are named using a convention that incorporates both experiment number and treatment. Example: 407_WL, 407_WW, 401_20-1, 401_20-2, 401_80
+    Directories are named using a convention that incorporates both experiment number and treatment. Example: 407_WL, 407_WW, 401_20-1, 401_20-2, 401_80
 
-#### Interim Data Product
+    #### Interim Data Product
 
 
-The interim data product consists of three primary components:
-- Masterfile (`Hyperspectral_data_AAPF_experiment_{Experiment_No}.xlsx`): This file stores the derived phenotypic measurements of the plants and a guide document.
-- HSI Data Processing Quality Control Data (`quality_control`): This directory contains information for quality assessment of the HSI data processing pipeline. It includes summaries of header information for plants, white and dark reference, a detailed record of the processing procedures employed, and animated gif files used to check coregistration quality between visible and near infrared (VNIR) and shortwave infrared (SWIR) data.
+    The interim data product consists of three primary components:
+    - Masterfile (`Hyperspectral_data_AAPF_experiment_{Experiment_No}.xlsx`): This file stores the derived phenotypic measurements of the plants and a guide document.
+    - HSI Data Processing Quality Control Data (`quality_control`): This directory contains information for quality assessment of the HSI data processing pipeline. It includes summaries of header information for plants, white and dark reference, a detailed record of the processing procedures employed, and animated gif files used to check coregistration quality between visible and near infrared (VNIR) and shortwave infrared (SWIR) data.
 
 
-- Compressed Vegetation Index Images (`{Vegetation_Index_Type}_{ROI filter}.zip: This section houses compressed image files for various types of vegetation indices calculated from the HSI data (ROI: region of interest).
+    - Compressed Vegetation Index Images (`{Vegetation_Index_Type}_{ROI filter}.zip: This section houses compressed image files for various types of vegetation indices calculated from the HSI data (ROI: region of interest).
 
 
 
 Animated gif files are included to check the coregistration quality between VNIR and SWIR data per each scan.
 
 Co-registration quality between VNIR and SWIR data for each scan is visually assessed using animated GIFs
 
-- Example:
-
-    401
-    ├── Hyperspectral_data_AAPF_experiment_401.xlsx (masterfile)
-    ├── quality_control
-    │   ├── header_summary_plants.csv
-    │   ├── header_summary_ref.csv
-    │   ├── HSI_R_2401761_240514080207482_VNIR-SIDE-DAT_401_20-1_240514080219626.gif
-    │   ├── HSI_R_2401761_240514080207482_VNIR-TOP-DAT_401_20-1_24051408022152.gif
-    │   ├── HSI_R_2401761_24061408172718_VNIR-SIDE-DAT_401_20-1_240614081746352.gif
-
-
-
-└── VI_images
-
+    - Example:
+
+        401
+        ├── Hyperspectral_data_AAPF_experiment_401.xlsx (masterfile)
+        ├── quality_control
+        │   ├── header_summary_plants.csv
+        │   ├── header_summary_ref.csv
+        │   ├── HSI_R_2401761_240514080207482_VNIR-SIDE-DAT_401_20-1_240514080219626.gif
+        │   ├── HSI_R_2401761_240514080207482_VNIR-TOP-DAT_401_20-1_24051408022152.gif
+        │   ├── HSI_R_2401761_24061408172718_VNIR-SIDE-DAT_401_20-1_240614081746352.gif
+        └── VI_images
+            ├── NDVI_default.zip
+            ├── NDWI_default.zip
+            ├── NLI_default.zip
+            └── NMDI_default.zip
 
 The data includes RGB and fluorescence images of plants along with derived morphological measurements and phenotypic information. Here's an example breakdown: