Repository files navigation

This repository contains Python scripts for converting raw OCT (Optical Coherence Tomography) files from Heidelberg Spectralis devices into TIFF volumes, primarily using the oct-converter package (https://github.com/marksgraham/OCT-Converter). These scripts were developed to process specific datasets from Heidelberg Spectralis OCT machines.

• .e2e files (Heidelberg Spectralis export format)
• .vol files (Heidelberg raw volume format)
• .fda files (Heidelberg raw data format)

pip install oct-converterpip install numpypip install tifffilepip install scikit-image

Each script follows the same command-line interface pattern:

python scripts/convert_e2e_to_tiff.py /path/to/input/directory /path/to/output/directorypython scripts/convert_vol_to_tiff.py /path/to/input/directory /path/to/output/directorypython scripts/convert_fda_to_tiff.py /path/to/input/directory /path/to/output/directory

The scripts will:

Recursively search through the input directory for files of the respective formatMaintain the directory structure in the output locationConvert each file to a TIFF volumeApply contrast enhancement using a double square root transformationSave the processed volumes as float32 TIFF files

These scripts were specifically developed for Heidelberg Spectralis OCT dataYou may need to modify the scripts to work with your specific OCT data format or structureThe contrast enhancement (log transformation) is applied to make features more visible - remove or modify this if not suitable for your analysisDirectory structure from the input is preserved in the output

These scripts are shared as-is, primarily as a reference for others working with Heidelberg Spectralis OCT data. They may require modification to work with different versions of the file formats or different OCT machines.

This repository is licensed under the MIT License (See License Info). If you are intending to use this repository for commercial use cases, please check the licenses of all Python packages used.