feat(docs): add initial README for CZI to Ilastik processing pipeline

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.

CHANGELOG.md

@@ -2,12 +2,25 @@
 
 ## [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.

README.md

+# Automated CZI to Ilastik Processing Pipeline
+
+### Author: Pierre Tocquin (University of Liège)
+
+---
+
+## Overview
+
+This script automates the processing of microscopy images in the CZI format. It provides functionalities to:
+- Convert CZI files into mosaics stored as TIFF files.
+- Perform segmentation of the mosaics using **Ilastik** in headless mode.
+- Correct segmentation issues, including:
+  - Identifying and preserving true nodes of Ranvier based on size and shape.
+  - Filling interruptions in nerve segments caused by gaps in segmentation.
+  - Applying morphological operations to refine segmentation results.
+- Resize both original and segmented outputs for downstream analysis.
+- Optimize disk usage by removing intermediate files.
+
+---
+
+## Features
+
+1. **Mosaic Assembly**: Converts tiled CZI images into complete mosaics stored as TIFF files.
+2. **Segmentation**: Leverages Ilastik for pixel classification in headless mode.
+3. **Segmentation Correction**:
+   - Preserves true nodes of Ranvier based on cluster size and aspect ratio.
+   - Removes thin or irregular structures via morphological operations.
+   - Fills white gaps in blue regions (nerve interruptions).
+4. **Resizing**: Scales the original and segmented images according to user-defined factors.
+5. **Intermediate File Cleanup**: Removes intermediate TIFF files to save disk space.
+
+---
+
+## Dependencies
+
+### Python Libraries:
+- [PyYAML](https://pyyaml.org/): For reading the YAML configuration file.
+  ```bash
+  pip install pyyaml
+  ```
+- [aicspylibczi](https://pypi.org/project/aicspylibczi/): For handling CZI files.
+  ```bash
+  pip install aicspylibczi
+  ```
+- [tifffile](https://pypi.org/project/tifffile/): For managing TIFF files.
+  ```bash
+  pip install tifffile
+  ```
+- [OpenCV](https://opencv.org/): For image resizing and morphological operations.
+  ```bash
+  pip install opencv-python-headless
+  ```
+
+### Ilastik:
+- Ilastik must be installed for pixel classification in headless mode.
+- [Download Ilastik](https://www.ilastik.org/download.html).
+
+---
+
+## Setup
+
+### Clone the repository:
+```bash
+git clone <repository-url>
+cd <repository-directory>
+```
+
+### Install dependencies:
+```bash
+pip install -r requirements.txt
+```
+*(Alternatively, install the dependencies manually as listed above.)*
+
+### Prepare the configuration file:
+Create or edit a YAML file (e.g., `config.yaml`) with the following parameters:
+```yaml
+output_dir: ./output
+compression: lzw
+resize_factor: 0.25
+project: /path/to/ilastik_project.ilp
+ilastik: /path/to/ilastik_executable
+area_threshold: 50
+closing_kernel_size: 11
+aspect_ratio_min: 1.5
+aspect_ratio_max: 5
+```
+
+---
+
+## Usage
+
+Run the script with the following command:
+
+```bash
+python process_pipeline.py file1.czi file2.czi ... --config /path/to/config.yaml
+```
+
+### Command-Line Arguments:
+- `file1.czi file2.czi ...`: List of CZI files to process.
+- `--config /path/to/config.yaml`: Path to the configuration file.
+
+### Example:
+```bash
+python process_pipeline.py sample1.czi sample2.czi --config config.yaml
+```
+
+---
+
+## How It Works
+
+1. **CZI File Processing**:
+   - The script reads tiled data from the CZI file and assembles it into a mosaic saved as a TIFF.
+
+2. **Segmentation**:
+   - The mosaic is passed to Ilastik in headless mode for segmentation.
+
+3. **Segmentation Correction**:
+   - **Red Cluster Filtering**: Red clusters (representing nodes of Ranvier) are identified based on:
+     - Minimum area (`area_threshold`).
+     - Aspect ratio (`aspect_ratio_min`, `aspect_ratio_max`).
+   - **Morphological Refinement**:
+     - Thin structures are removed using erosion + dilation.
+     - Interruptions in nerve segments are filled with morphological closing.
+
+4. **Image Resizing**:
+   - Both the original mosaic and segmented outputs are resized using a scaling factor (`resize_factor`).
+
+5. **Intermediate File Cleanup**:
+   - Intermediate TIFF files are removed to save disk space.
+
+---
+
+## Configuration Parameters
+
+| Parameter            | Description                                                                 | Example                |
+|----------------------|-----------------------------------------------------------------------------|------------------------|
+| `output_dir`         | Directory where processed files are saved.                                 | `./output`            |
+| `compression`        | Compression type for TIFF files.                                           | `lzw`                 |
+| `resize_factor`      | Scaling factor for resizing images.                                        | `0.25`                |
+| `project`            | Path to the Ilastik project file (`.ilp`).                                 | `/path/to/project.ilp`|
+| `ilastik`            | Path to the Ilastik executable.                                            | `/path/to/ilastik`    |
+| `area_threshold`     | Minimum size of red clusters (nodes of Ranvier).                           | `50`                  |
+| `closing_kernel_size`| Kernel size for filling interruptions in blue regions (nerve segments).    | `11`                  |
+| `aspect_ratio_min`   | Minimum aspect ratio for identifying true nodes of Ranvier.                | `1.5`                 |
+| `aspect_ratio_max`   | Maximum aspect ratio for identifying true nodes of Ranvier.                | `5`                   |
+
+---
+
+## Output Files
+
+- **Original TIFF**: The assembled mosaic from the input CZI file.
+- **Segmented TIFF**: The output from Ilastik after pixel classification.
+- **Corrected TIFF**: The segmented image after corrections for segmentation issues.
+- **Resized TIFFs**: Resized versions of the original and segmented images.
+
+---
+
+## Troubleshooting
+
+1. **Error: Ilastik not found**:
+   - Ensure the path to the Ilastik executable is correct in the configuration file.
+
+2. **FileNotFoundError for CZI files**:
+   - Verify the input file paths and ensure they exist.
+
+3. **Incorrect segmentation**:
+   - Adjust the `area_threshold`, `aspect_ratio_min`, and `aspect_ratio_max` in `config.yaml`.
+
+---
+
+## License
+
+This project is licensed under the MIT License. See the `LICENSE` file for details.