The newly added README provides a comprehensive overview of the automated pipeline for processing microscopy images from CZI format to TIFF, including segmentation using Ilastik. It details features, setup instructions, dependencies, usage guidelines, and troubleshooting tips, significantly improving documentation and aiding user understanding and implementation of the process.

Introduced `process_pipeline.py` to automate conversion of CZI images to TIFF, perform analysis with Ilastik, and resize outputs based on YAML configuration. Updated dependencies in `requirements.txt` to support new functionality.

Switched from using OpenCV (cv2) to Tifffile for reading images, specifically TIFF files, in the resize_image function to better handle multi-dimensional image data. The change was made due to Tifffile's superior capabilities in dealing with TIFF images compared to OpenCV. Additionally, removed unnecessary resizing before Ilastik processing to streamline the workflow and avoid redundancy. This update aims to improve workflow efficiency and maintain image quality handling in microscopy applications.