Follicle Separation

A simple GUI application for processing 3D segmentation data and separating follicles using morphological operations and watershed segmentation.

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Installation

Make sure you have Python 3.9+ installed.

Install the package using pip:

pip install git+https://github.com/guignardlab/follicleseparation

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Running the App

After installation, launch the GUI:

follicle-separation

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How to Use

1. Select Input Folder

   • Contains .h5 segmentation files.

2. Set File Formats

   • Intensity Format (currently unused but required):

     time_{t:03d}_zstack_10-24.h5
     

   • Segmentation Format:

     time_{t:03d}_zstack_10-24-data_Simple Segmentation.h5
     

3. Set Outside Label

   • Integer label corresponding to the background (default: 3).

4. Select Output Folder

   • Results will be saved as .tiff files.

5. Run Separation

   • Click "Run Separation" to process all timepoints.

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Input Requirements

• HDF5 files (.h5) must contain:

  /exported_data
  

  with segmentation labels in the first channel.

• Filenames must include a time index formatted like:

  time_XXX
  

  where XXX is a zero-padded integer.

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Output

For each timepoint, a file is generated:

result_time_XXX.tiff

Each output contains labeled regions after watershed-based separation.

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Notes

• The algorithm:

  • Extracts the largest connected background component
  • Identifies nuclei regions
  • Computes a distance transform
  • Applies watershed segmentation

• Processing is done per timepoint automatically.

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Troubleshooting

• No files processed

  • Check filename patterns match the expected format.

• GUI not opening

  • Ensure tkinter is installed.

• Errors during processing

  • Verify .h5 file structure and labels.

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License

MIT (or specify your license)