This script processes HDF5 files containing 3D datasets and converts them to TIFF stacks. It includes a simple GUI built with Tkinter to select the input and output directories and provides options to process either a single folder or all subfolders.
- Select an input folder containing HDF5 files and Luxendo JSON metadata files.
- Convert HDF5 files to TIFF stacks with proper voxel dimensions.
- Process files in a single folder or recursively through all subfolders.
- Maintain the original folder structure for output files in multi-folder processing mode.
Before running the script, ensure you have the following installed:
- Python 3.x
- Required Python packages:
h5py,tifffile
You can install the required packages using pip:
pip install h5py tifffile- Starting the Script: Run the script using your IDE (Visual Studio/pyCharm/etc.), A GUI will appear.
- Optional: You can run the script in its
.exeform without IDE,- download here: luxendo-h5-converter-v4
- Optional: You can run the script in its
Note
Windows might flag this file as a risk. Once you see the warning, you can click on More info and then Run anyway to use this program.
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Selecting Directories:
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Process Single Folder:
- Click the "Process Single Folder" button.
- Select the input folder containing the HDF5 files.
- Select the output folder where the TIFF files will be saved.
- The script will process all HDF5 files in the selected input folder and save the converted TIFF files in the output folder.
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Process Entire Directory Tree:
- Click the "Process Entire Directory Tree" button.
- Select the input folder containing the HDF5 files.
- The script will process all HDF5 files in the selected folder and all its subfolders.
- The converted TIFF files will be saved in their corresponding original folders within the input directory.
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Monitoring Progress: The GUI window will display the processing status, including the current folder and file being processed.
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Completion: a message will be displayed in the status window once processing is complete.