Nextflow Workflow
If you have access to a Linux or Mac-OS machine you can use nextflow to run the processing steps automatically. We will demonstrate this on the raw_data/BBBC02 dataset.
Build Config
The first step is to build the config file. To this end you must run the following command:
You will be asked a series of questions. Select the following answers:
Select the raw_data dir:/path/to/example-project/raw_data/BBBC002_v1_images/drosophila_kc167_1_images/Enter the suffix of the files to process:.TIFSelect the output dir:/path/to/example-project/processed_data
Run Workflow
The next step is to run the nextflow workflow. To this end you must run the following command:
The workflow will execute s01_segment followed by s02_measure and write the outputs to processed_data/drosophila_kc167_1_images/s01_segment and processed_data/drosophila_kc167_1_images/s02_measurements respectively.
Nextflow Execution
The nextflow workflow is executed in the WD directory and nextflow will create a .nextflow and work directory, which are used by nextflow to manage the workflow execution. A detailed nextflow log file is written to runs/BBBC02/.nextflow.log.
Visualize Results
The final step is to visualize the results. To this end you must run the following command:
In the jupyter notebook that opens you can select the experiment and image to visualize. The notebook will display the original image, the segmented nuclei, and the extracted measurements in napari.
