harmony-to-organoid 0.1.0

Utility for extracting individual organoid max projections from the export of Opera Phenix Harmony software.

Harmony to Organoid

Example output

Check out this page for exemplary output files.

How to Prepare

1. Install UV
   Follow the installation guide for UV.

2. Initial Setup
   Running the tool for the first time will automatically install all necessary dependencies.

How to Run

How to run from commandline

Process your data exported from Harmony by executing the following command:

Parameters:

• --index-file: (Required) Path to the Harmony export index XML file (Index.idx.xml) or (Index.xml) located next to the corresponding TIFF files.
• --output-dir: (Required) Path to your desired output directory.
• --lut-min: (Optional) Comma-separated minimum LUT (Lookup Table) values for each channel.
• --lut-max: (Optional) Comma-separated maximum LUT values for each channel.
• --colors: (Optional) Comma-separated colors for each channel.

Example:

uv run https://gitlab.com/ida-mdc/harmony-to-organoid/-/raw/main/script.py process \
    --index-file MY/INPUT/DATA/Index.xml \
    --output-dir MY/OUTPUT/DATA \
    --lut-min 100,100,100,100 \
    --lut-max 2000,1000,1500,2000 \
    --colors white,orange,blue,#ff0000

Output:

After successfully running the processing command, your specified output directory (MY/OUTPUT/DATA) will contain the following:

• Projections:
  Maximum intensity projection images (projections/) generated for each data group, providing 2D summaries of your 3D data.

• Plots:
  Visual representations of the data are stored in plots, including group bounding boxes and projections placed within their respective areas, ensuring spatial consistency and aiding in data interpretation.

• README Files:
  Automatically generated documentation (README.md and README.html) that includes embedded plots for easy reference and sharing.

How to run from Jupyter notebook

micromamba activate YOUR_ENVIRONMENT
pip install