4- Puncta Extraction

This section describes the process of puncta extraction in the ExSeq-Toolbox. It involves extracting puncta from images, consolidating channel information, and preparing data for subsequent analysis steps.

Step 1: Load Configuration Settings

Begin by initializing and loading the configuration settings.

from exm.args.args import Args

# Initialize the Args object for configuration.
args = Args()

# Provide the path to the configuration file.
args_file_path = '/path/to/your/parameter/file.json'

# Load the configuration settings from the file.
args.load_params(args_file_path)

# Ensure the correct configuration file path.

Step 2: Puncta Extraction

Extract puncta using specified parameters and configuration settings.

from exm.puncta.extract import extract

# Define the list of Code, FOV pairs for extraction.
code_fov_pairs_to_extract = [(code_val, fov_val) for code_val in args.codes for fov_val in args.fovs]

# Parameters for extraction.
use_gpu_setting = True
num_gpus = 3
num_cpus = 3

extract(args=args,
        code_fov_pairs=code_fov_pairs_to_extract,
        use_gpu=use_gpu_setting,
        num_gpu=num_gpus,
        num_cpu=num_cpus)

Step 3: Channel Consolidation

Consolidate extracted channel information.

from exm.puncta.consolidate import consolidate_channels

# Parameters for channel consolidation.
num_cpus_for_channel = 4

consolidate_channels(args=args,
                     code_fov_pairs=code_fov_pairs_to_extract,
                     num_cpu=num_cpus_for_channel)

Step 4: Code Consolidation

Consolidate codes for the analysis.

from exm.puncta.consolidate import consolidate_codes

# Parameters for code consolidation.
fov_list_to_consolidate = list(args.fovs)
num_cpus_for_code = 4

consolidate_codes(args=args, fov_list=fov_list_to_consolidate, num_cpu=num_cpus_for_code)

# Monitor logs or console output for processing errors.

Next Steps

Following the completion of puncta extraction and consolidation, the next phase in the ExSeq-Toolbox workflow is Puncta Basecalling. This step is vital for interpreting the extracted data in biological context. For detailed instructions on Puncta Basecalling, refer to the Puncta Basecalling section of this guide.