1- Pipeline Configuration

This tutorial covers the initial setup and configuration for the ExR dataset. It is an essential first step to correctly prepare the environment and data paths for subsequent processing.

Step 1: Import Libraries and Initialize Configuration

Start by importing necessary libraries and initializing the configuration object.

import numpy as np
from exr.config.config import Config

# Initialize the configuration object.
config = Config()

Step 2: Set Mandatory Configuration

Define the mandatory settings, particularly the path to your raw data directory.

raw_data_directory = '/Path/to/your/raw_data/'

Step 3: Define Raw Data Directory Structure

Ensure your raw data adheres to the required directory structure.

# RawDataDir/
# ├── R1/
# │   ├── ROI1.nd2
# │   ├── ROI2.nd2
# │   └── ...
# ├── R2/
# │   ├── ROI1.nd2
# │   ├── ROI2.nd2
# │   └── ...
# ├── R3/
# │   └── ...
# └── ...

Step 4: Specify Optional Configuration

Adjust optional settings such as the number of rounds, ROIs, and pixel spacing.

# Define the number of rounds in the ExR dataset.
# By default, we set it to 12 rounds, but you can adjust this as needed.
num_rounds = 12

# Define the number of regions of interest (ROIs).
# This might vary depending on the dataset.
num_rois = 4

# The absolute path to the processed data directory.
# By default, a 'processed_data' subdirectory inside the raw_data_path is used.
processed_data_directory = '/path/to/processed/data/'

# Spacing between pixels in the format [Z,Y,X].
# Adjust these values according to your experimental setup.
pixel_spacing = [0.250, 0.1625, 0.1625]

# Set the names of channels in the ND2 file.
# Adjust these names according to your experimental setup.
channel_names_list = ['640', '561', '488']

# Reference round number. Adjust based on your experiment.
reference_round = 1

# Reference channel name. Adjust based on your experiment.
reference_channel = '640'

# Provide the name for the configuration file.
# It's recommended to provide a meaningful name related to the dataset or experiment.
config_file = "your_config_name"

# If set to True, changes permission of the processed data to allow other users to read/write.
permissions_flag = False

# If set to True, creates the directory structure in the specified project path.
create_directory_structure_flag = True

Step 5: Apply Configuration Settings

Apply the configuration settings using the set_config method.

config.set_config(
raw_data_path=raw_data_directory,
processed_data_path=processed_data_directory,
rounds=list(range(1, num_rounds+1)),
rois=num_rois,
spacing=pixel_spacing,
channel_names=channel_names_list,
ref_round=reference_round,
ref_channel=reference_channel,
permission=permissions_flag,
create_directory_structure=create_directory_structure_flag,
config_file_name=config_file
)

# Note: Always verify the correctness of paths and parameters before running.

Next Steps

After completing the initial configuration, the next step is to proceed to Volume Alignment. For details on performing volume alignment, refer to the Volume Alignment section of this guide.