iSyntax2TIFF Converter

A tool for converting Philips iSyntax whole slide images to TIFF format, with support for batch processing and pyramidal TIFF generation.

Overview

This tool provides functionality to:

1. Convert iSyntax (.i2syntax) files to OME-TIFF format
2. Generate pyramidal TIFF files from OME-TIFF
3. Process multiple files in batch using SLURM workload manager

Prerequisites

• SLURM workload management system
• Required environment dependencies (see Environment Setup)

Environment Setup

Please follow the installation instructions in the environment_installment folder to set up all required dependencies.

Usage

1. Generate Input File List

Create a list of iSyntax files to process:

find /path/to/isyntax/folder -maxdepth 1 -type f -name "*.i2syntax" | sort > input_list.txt

Replace /path/to/isyntax/folder with the actual path to your iSyntax files.

2. Convert iSyntax to OME-TIFF

1. Open batchrun.sh and adjust the array job parameters in line 10 to match your number of files
2. Submit the batch job:

   sbatch batchrun.sh

3. Convert OME-TIFF to Pyramidal TIFF

Submit the conversion job:

sbatch batchrun_ome2pyramidal.sh

Note: Integration of steps 2 and 3 into a single workflow is planned for future updates.

File Structure

• batchrun.sh - SLURM script for iSyntax to OME-TIFF conversion
• batchrun_ome2pyramidal.sh - SLURM script for OME-TIFF to pyramidal TIFF conversion
• environment_installment/ - Environment setup instructions and scripts

Contributing

Feel free to submit issues and enhancement requests.

License

[Specify your license here]