1- Pipeline Parameter Configuration

This step focuses on configuring the pipeline parameters for the ExSeq-Toolbox. The process involves setting up the logger, initializing configuration objects, and defining mandatory and optional configuration parameters.

Step 1: Import Modules and Configure Logger

First, import the necessary modules and configure the logger:

from exm.utils.log import configure_logger
from exm.args.args import Args

# Configure logger for ExSeq-Toolbox
logger = configure_logger('ExSeq-Toolbox')

Step 2: Initialize Configuration Object

Initialize the configuration object to hold all pipeline parameters:

# Initialize the configuration object.
args = Args()

Step 3: Mandatory Configuration

Set the absolute path to the raw data directory. This is a required setting:

raw_data_directory = '/path/to/your/raw_data_directory/'

Step 4: Raw Data Directory Structure

The ExSeq-Toolbox assumes a specific directory structure for raw data:

# Ensure that your raw data adheres to this directory structure before running the package.
# raw_data_directory/
    # ├── code0/
    # │   ├── Channel405 SD_Seq0004.nd2
    # │   ├── Channel488 SD_Seq0003.nd2
    # │   ├── Channel561 SD_Seq0002.nd2
    # │   ├── Channel594 SD_Seq0001.nd2
    # │   ├── Channel604 SD_Seq0000.nd2
    # ├── code1/
    # │   ├── Channel405 SD_Seq0004.nd2
    # │   ├── ...
    # ├── ...

Step 5: Optional Configuration

Define additional optional configuration parameters like codes_list, fov_list, and others:

codes_list = list(range(7))
fov_list = list(range(12))  # Example values
...

Step 6: Set Parameters

Finally, set the parameters using the set_params method of the args object:

args.set_params(
    raw_data_path=raw_data_directory,
    ...
    args_file_name=args_file
)

# Note: Always ensure that the paths and other configuration parameters are correct before running the script.

Next Steps

After configuring the pipeline parameters, the next step is to proceed to Volume Alignment. For details on how to perform volume alignment, refer to the Volume Alignment section of this guide.