directionality-quantification 0.1.0

Package for cell directionality quantification.

Cell Extension Orientation

How to install

Tested with Python 3.11.

git clone https://gitlab.com/ida-mdc/directionality-quantification.git
cd directionality-quantification
pip install -e .

How to use

List arguments:

cell-extension-orientation --help

Example use case:

directionality-quantification --input_raw sample/input_raw.tif --input_labeling sample/input_labels.tif --input_target 
sample/input_target.tif --output sample/result --pixel_in_micron 0.65 --output_res 7:10

Generate exemplary output on sample data via unit test:

python -m unittest tests/test_sample.py

Step-by-Step Workflow

1. Parse Input Arguments

• The script accepts various user-defined arguments, including:
  • Raw image and segmentation label map (required).
  • Optional parameters like ROIs, mask images, cell tables, and output settings.
• Arguments control preprocessing, analysis filters (e.g., size thresholds), and visualization options.

2. Load Input Data

• Reads the raw microscopy image and segmentation label map using tifffile.
• Optionally, loads:
  • A binary mask for specific regions.
  • A cell table with predefined properties for analysis.

3. Crop Images to ROI

• If ROIs are specified, the script extracts subregions of the raw image, label map, and mask for focused analysis.

4. Segment and Label Regions

• Segmentation regions are labeled using connected component analysis (label).
• The script identifies individual objects (cells) for further analysis.

5. Filter Regions

• Filters segmented regions based on:
  • Minimum Size: Excludes regions below a specified pixel count.
  • Maximum Size: Excludes regions exceeding a specified pixel count.

6. Analyze Each Segment

For each segmented region:

1. Skeletonization:
   • Generates the skeleton (centerline) of the region to identify structure and direction.
2. Distance Map:
   • Calculates the distance of each pixel to the nearest boundary (used for determining the region's center).
3. Identify Key Points:
   • Locates the central pixel and categorizes pixels as "inside" or "outside" the region relative to the center.
4. Direction Calculation:
   • Computes the mean directional vector for extensions outside the region.
   • Optionally, calculates directional vectors relative to a target distance map if provided.

7. Store Results

• For each region, records:
  • Direction vector length.
  • Absolute angle of the direction vector.
  • Relative angle compared to the target vector (if applicable).
  • Stores results in the cell table if provided.

8. Generate Visualizations

• Plots include:
  • All Directions: Visualizes individual cell extensions with directional arrows.
  • Average Directions: Computes average directions in user-defined tiles and visualizes them with heatmaps.
  • ROIs: Highlights selected regions of interest.

9. Save Outputs

• Results are saved to the specified output folder:
  • CSV File: Contains cell-level analysis metrics.
  • Images: Includes plots of directions, average directions, and ROIs.

Outputs

1. CSV File

• A CSV file named cells.csv is generated in the output directory (if a cell table is provided or regions are analyzed).
• The file contains the following columns:

Column Name	Description
length_cell_vector	Length of the calculated directional vector for the cell extension.
absolute_angle	Absolute angle of the directional vector in radians relative to the vertical axis.
rolling_ball_angle	Angle of the directional vector relative to a target map (if provided).
relative_angle	Angle between the directional vector and the target vector (if applicable).

• If an input cell table is provided, these columns are appended to it, preserving the existing structure.

2. Visualization Outputs

• Saved as image files in the specified output folder. The exact outputs depend on the options provided:

1. All Directions (directions_<region>.png):

   • Visualizes individual cell extension vectors for each region.
   • Directional arrows are color-coded by angle or relative directionality (if a target map is used).

2. Average Directions (directions_<region>_tile<size>.png):

   • Computes and visualizes average directional vectors within tiles of a specified size (e.g., 100px, 250px).
   • Heatmap-like visualization where tile colors represent average directions and lengths.

3. ROIs (ROIs.png):

   • Highlights the selected regions of interest with color-coded bounding boxes.

TODO Past calls

album run de.oncoray:cell-orientation:0.1.0-SNAPSHOT --input_raw "/home/deschmi/Development/album/data/Sindi Nexhipi/relative/Microglia Segmentation P2_A_C3H_M3-0008.czi_Scene2.tif" --input_labeling "/home/deschmi/Development/album/data/Sindi Nexhipi/relative/Microglia Segmentation P2_A_C3H_M3-0008.czi_Scene2.tif" --input_target "/home/deschmi/Development/album/data/Sindi Nexhipi/relative/Ventricles P2_A_C3H_M3-0008-2.tif" --output "/home/deschmi/Development/album/data/Sindi Nexhipi/relative/24_output" --pixel_in_micron 0.65 --output_res 7:10 --roi 10500:15000:9900:14000,12300:13000:12500:13300