Workflow: Cell Counting¶
This workflow demonstrates how to count cells in a fluorescence microscopy image.
Pipeline Overview¶
Image Reader → Gaussian Blur → Binary Threshold → Remove Small Obj → Watershed → Data Table
Step-by-Step¶
1. Load the Image¶
Add an Image Reader node and select your microscopy image.
2. Pre-process¶
- Gaussian Blur (sigma = 1-2): Reduces noise
- Equalize Adapthist (optional): Enhances contrast for uneven illumination
3. Segment¶
- Binary Threshold: Separate cells from background. Adjust the threshold until cells are cleanly separated.
- Remove Small Obj: Eliminate noise artifacts (set minimum size in pixels)
4. Split Touching Cells¶
- Watershed: Separates touching/overlapping cells using distance-based markers
- Set Min Object Sep. to the approximate minimum distance between cell centers
5. Measure¶
The Watershed node outputs both a label image and a table with per-object measurements:
- Area, perimeter, circularity
- Centroid coordinates
- Eccentricity, orientation
- Intensity statistics (if image is connected)
6. Visualize¶
Connect the table to a Data Table Node for inline viewing, or to plot nodes for visualization.