# Changelog ## [Unreleased] - 2024-12-02 ### Enhanced - **process** - **Enhancement:** Segmentation correction with additional parameters. - Added new configuration options: `area_threshold`, `closing_kernel_size`, `aspect_ratio_min`, and `aspect_ratio_max` for improved segmentation correction. - These changes help in preserving true nodes of Ranvier by filtering based on cluster size and aspect ratio. - Introduced morphological operations to fill interruptions in nerve segments. - Updated the function and documentation to reflect these enhancements. - Overall, this improves the accuracy and reliability of image segmentation results. ### Refactored - **refactor(image-processing):** Replace cv2 with Tifffile for reading large images to prevent CV_IO_MAX_IMAGE_PIXELS exception with cv2. - Switched from using OpenCV (cv2) to Tifffile for reading images, specifically TIFF files, in the `resize_image` function. - This change was made due to Tifffile's superior capabilities in handling multi-dimensional image data compared to OpenCV. - Removed unnecessary resizing before Ilastik processing to streamline the workflow and avoid redundancy. - The update aims to improve workflow efficiency and maintain image quality handling in microscopy applications. - **refactor(pipeline):** Using the filename without extension for generating TIFF files. - This change extracts the base name of the file without its extension when creating output TIFF files. - Previously, the full path with extension was used, which could lead to redundant extensions in output filenames. - This update ensures clearer and more concise naming conventions for generated files. ### Added - **feat(image-processing):** Add script for batch processing and resizing images with Ilastik. - This new script automates the process of running Ilastik in headless mode for image segmentation while resizing input and output images. - Input images are resized using quality-preserving interpolation, whereas segmented outputs use nearest-neighbor interpolation to maintain segmentation integrity. - It is designed to handle large batches of images efficiently, supporting user-specified scale factors and ensuring ease of use with command-line arguments. - **feat(pipeline):** Add script for automating CZI to TIFF processing and analysis. - Introduced `process_pipeline.py` to automate conversion of CZI images to TIFF. - Integrated analysis with Ilastik and resizing outputs based on YAML configuration. - Updated dependencies in `requirements.txt` to support new functionality. ## [Unreleased] - 2024-12-01 ### Added - Script for converting czi mosaic to tif - Script for running Ilastik in headless mode