iSyntaxToTIFF

Standalone tool to convert Philips .isyntax whole-slide images to pyramidal RGB OME-TIFF using OpenPhi and the Philips Pathology SDK.

The application is designed as a focused iSyntax converter, separate from TiffCropper, so that iSyntax support can remain isolated from the standard crop, preview, tile, merge, and visualization workflows.

What this app does

• Configure the Philips Pathology SDK path from the graphical interface.
• Test the required SDK imports in the correct order.
• Preview a small thumbnail of .isyntax files.
• Convert .isyntax files to pyramidal .ome.tif files.
• Use Deflate lossless compression by default.
• Optionally use JPEG compression with quality control.
• Save a CSV conversion log.
• Support Windows and Linux builds, depending on the corresponding Philips Pathology SDK package.

Philips Pathology SDK requirement

This application requires the Philips Pathology SDK to read .isyntax files. The SDK should be obtained separately from Philips and configured from the application menu.

As of June 2026, the Philips Pathology SDK can be accessed from:

https://philips.mizecx.com/login.html

A possible access route is to enter as GuestUser, search for PathologySDK, and download the package named:

PathologySDK_2.0-L1_Packages

Inside that package, Philips provides operating-system-specific SDK archives. Use the research Python package that matches your operating system and Python compatibility:

Windows: Philips Pathology SDK for Windows / Python 3.7 research package
Linux:   Philips Pathology SDK for Ubuntu 20.04 / Python 3.8 research package

After downloading and extracting the appropriate SDK package, open iSyntaxToTIFF and configure the SDK folder from:

File > Select / Prepare SDK folder

Then run:

File > Test SDK

Expected SDK test result:

pixelengine OK
softwarerenderbackend OK
softwarerendercontext OK
OpenPhi OK
Ready for iSyntax conversion

Recommended workflow for end users

1. Download the latest iSyntaxToTIFF release for your operating system.
2. Extract the downloaded archive.
3. Run the application.
4. Download and extract the Philips Pathology SDK package that matches your operating system.
5. In the app, go to File > Select / Prepare SDK folder.
6. Select the Philips SDK root folder.
7. Use File > Run SDK installer if the SDK has not been installed or prepared before.
8. Use File > Test SDK.
9. Add .isyntax files.
10. Preview selected files if desired.
11. Convert them to pyramidal OME-TIFF.

If no output folder is selected, the converted .ome.tif file will be saved beside each input .isyntax file. To set a specific output folder, use:

File > Set output folder

Recommended conversion settings

For maximum fidelity relative to the rendered RGB image produced by OpenPhi:

Compression: Deflate lossless
Tile size: 512
Max pyramid levels: 8
Minimum pyramid dimension: 1024
View: display

JPEG compression is optional and produces smaller files, but it is lossy. JPEG quality defaults to 100 when selected.

Important modality note

The output is lossless only with respect to the rendered RGB image returned by OpenPhi. This is suitable for visual brightfield workflows such as H&E/IHC conversion, preview, tiling, annotation, and QuPath viewing.

Do not assume that raw fluorescence channels or quantitative intensities are preserved unless this is validated independently against the original acquisition data and metadata.

Developer setup: Windows

The Windows build uses Python 3.7 because the tested Philips Pathology SDK Windows binaries require Python 3.7 compatibility.

Create the conda environment:

conda env create -f environment-windows.yml
conda activate isyntax_py37

Alternatively, install dependencies manually:

conda activate isyntax_py37
python -m pip install --upgrade "pip<24"
pip install -r requirements-windows-py37.txt

Run from source:

python src\isyntax_to_tiff\app.py

Build the Windows application locally:

build_windows_exe.bat

The output will be:

dist\iSyntaxToTIFF\iSyntaxToTIFF.exe

Distribute the full folder:

dist\iSyntaxToTIFF

not only the .exe, because PyInstaller --onedir builds require adjacent dependency files.

Developer setup: Linux

The Linux build targets the Ubuntu 20.04 / Python 3.8 Philips Pathology SDK research package.

Install Python dependencies in a Python 3.8 environment:

python3.8 -m venv .venv-isyntax-linux
source .venv-isyntax-linux/bin/activate
python -m pip install --upgrade pip
pip install -r requirements-linux-py38.txt

Run from source:

python src/isyntax_to_tiff/app.py

Build the Linux application locally:

chmod +x build_linux.sh
./build_linux.sh

The output will be:

dist/iSyntaxToTIFF/iSyntaxToTIFF

Package the Linux build:

tar -czf iSyntaxToTIFF-Linux.tar.gz -C dist iSyntaxToTIFF

GitHub Actions build

The workflow in .github/workflows/build.yml creates Windows and Linux application builds automatically.

Manual build:

GitHub > Actions > Build iSyntaxToTIFF > Run workflow

Release build:

git tag v1.0.0
git push origin v1.0.0

When a tag beginning with v is pushed, the workflow uploads the release artifacts, for example:

iSyntaxToTIFF-Windows.zip
iSyntaxToTIFF-Linux.tar.gz

## Citation

If you use **iSyntaxToTIFF** in your research, please cite:

Rodríguez-Rojas J. *iSyntaxToTIFF: A standalone converter for Philips iSyntax whole-slide images to pyramidal OME-TIFF*. Zenodo. 2026. https://doi.org/10.5281/zenodo.20798592

DOI: `10.5281/zenodo.20798592`

The citation metadata is also provided in [`CITATION.cff`](CITATION.cff) and [`.zenodo.json`](.zenodo.json).

License

MIT License for this application code.

The Philips Pathology SDK is separate software provided by Philips and is subject to Philips' own license terms.