Merge pull request #6 from zoccoler/rev1_b

Update notebooks with more descriptions and path to data in python script

Author: zoccoler

code/phasor_plot_AZ212.ipynb

@@ -1,3 +1,18 @@
+"""
+Batch processing script for FLIM phasor plot analysis of all embryo samples.
+This script processes all folders in the 'embryos_data' folder, extracting phasor plots,
+performing segmentation, and saving results in the respective output folders.
+
+Phasor-related inputs:
+- harmonic: 1
+- threshold: 15
+- binning: yes
+- binning in 3D: no
+- binning kernel size: 3x3
+- median filter: yes
+- number of median filter interations: 3
+"""
+
 import napari
 import tifffile
 import numpy as np
@@ -22,8 +37,9 @@
 start_time = time.time()
 # Inputs
 
-# Main folder path (each folder contains a zarr file and an xml file)
-main_folder_path = Path("../embryos_data/")
+# Data folder path called 'embryos_data' (each folder contains a zarr file and an xml file)
+# placed iside the repository root directory
+main_folder_path = Path(__file__).parent / '..' / 'embryos_data'
 
 # Additional manual metadata if xml file was not available (not the case)
 z_pixel_size = 0.5*1e-6 # in m
@@ -69,7 +85,7 @@
 store_phasor_mask = False
 
 processed_samples = []
-
+print(f"Starting batch processing of FLIM phasor plots in folder: {main_folder_path}")
 # Iterate throgh all the folders in the main folder
 for folder in main_folder_path.iterdir():
     new_sample_time = time.time()