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Step-by-Step Processing

The image processing and analysis steps can be executed one-by-one. We will demonstrate this on the raw_data/BBBC01 dataset.

Build Config

The first step is to build the config file. To this end you must run the following command:

WD=runs/BBBC01 pixi run build_config

$env:WD='runs/BBBC01'; pixi run build_config

set WD=runs/BBBC01
pixi run build_config

Environment Variable WD

The WD variable is used to specify the working directory. This is where the config file will be stored. Check the runs directory for the newly created BBBC01 directory containing the acquisition_config.yaml file.

You will be asked a series of questions. Select the following answers:

  • Select the raw_data dir: /path/to/example-project/raw_data/BBBC001_v1_images_tif/human_ht29_colon_cancer_1_images/
  • Enter the suffix of the files to process: .tif
  • Select the output dir: /path/to/example-project/processed_data

Edit Config

You can edit the config file with your favorite text edtior or re-run the pixi run build_config command to change the answers.

Next to the acquisition_config.yaml file you will find the githash.log file. This file contains a history of the executed pixi commands and the git hash of the project at the time of execution.

Run Segmentation

The first processing step is to segment the nuclei. To this end you must run the following command:

WD=runs/BBBC01 pixi run segment

$env:WD='runs/BBBC01'; pixi run segment

set WD=runs/BBBC01
pixi run segment

This will execute the first processing step and produce the following outputs:

  • processed_data/human_ht29_colon_cancer_1_images/s01_segmentation contains the segmented nuclei images.
  • runs/BBBC01/measure_config.yaml is the configuration file for the next processing step.
  • runs/BBBC01/<time-stamp>-segmentation.log contains the log of the segmentation step.

Extract Measurements

The second processing step is to extract measurements from the segmented nuclei. To this end you must run the following command:

WD=runs/BBBC01 pixi run measure

$env:WD='runs/BBBC01'; pixi run measure

set WD=runs/BBBC01
pixi run measure

This will execute the second processing step and produce the following outputs:

  • processed_data/human_ht29_colon_cancer_1_images/s02_measurement contains the extracted measurement csv files.
  • runs/BBBC01/<time-stamp>-measurement.log contains the log of the measurement step.
  • runs/BBBC01/measure_outputs.yaml contains a list of the measurement csv files.

Visualize Results

The final step is to visualize the results. To this end you must run the following command:

WD=runs/BBBC01 pixi run visualize

$env:WD='runs/BBBC01'; pixi run visualize

set WD=runs/BBBC01
pixi run visualize

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.

Result Visualization
A jupyter notebook with IPython Widgets to select experiment and image, which are then displayed in napari.