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.