harmony-to-organoid 0.4.0

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

You can install the tool via pip:

pip install harmony-to-organoid

How to Run

How to run from commandline

Process your data exported from Harmony by executing the command harmony-to-organoid process.

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.
• --align-fields: (Optional) Align fields using ashlar. True by default.
• --exclude-fields: (Optional) Comma separated list of field IDs which should not be processed.

Example:

harmony-to-organoid 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 \
    --exclude-fields 2,3,7

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

Check out our example notebook notebook.ipynb.