Skip to content
Snippets Groups Projects
Select Git revision
  • develop default protected
1 result
Blame Permalink
  • Pierre Tocquin's avatar
    2aa350f2
    feat(docs): add initial README for CZI to Ilastik processing pipeline · 2aa350f2
    Pierre Tocquin authored 
    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.
    2aa350f2
    History
    feat(docs): add initial README for CZI to Ilastik processing pipeline
    Pierre Tocquin authored 
    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.
Code owners
Assign users and groups as approvers for specific file changes. Learn more.
CHANGELOG.md 2.67 KiB

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