How to Count Cells in ImageJ

April 29, 2026

Counting cells in ImageJ is one of the most common tasks in biological image analysis. The standard approach uses thresholding to separate cells from background, then Analyze Particles to count distinct objects.

The Manual Method

1. Open your image

Go to File → Open and select your image. For best results use a grayscale image, or convert first via Image → Type → 8-bit.

2. Apply a threshold

Go to Image → Adjust → Threshold (or press Ctrl+Shift+T). Drag the sliders until cells are highlighted in red. Click Apply.

3. Convert to a binary mask

Go to Process → Binary → Make Binary. This converts your image to pure black and white — cells are black, background is white.

4. Run Analyze Particles

Go to Analyze → Analyze Particles. Set:

• Size (pixel²): A minimum that filters out noise (e.g. 50-Infinity)
• Circularity: 0.5-1.0 for roughly round cells
• Show: Outlines to preview detections
• Check Display results and Summarize

Click OK. The Summary table shows the total count.

Common Problems

• Too many small objects: Increase the minimum size in Analyze Particles.
• Cells merged together: Run Process → Binary → Watershed before Analyze Particles to split touching cells.
• Inconsistent threshold across images: Use Image → Adjust → Auto Threshold with Otsu for reproducible results.

ImageJ Macro for Batch Cell Counting

dir = getDirectory("Choose folder");
list = getFileList(dir);
for (i = 0; i < list.length; i++) {
    open(dir + list[i]);
    run("8-bit");
    setAutoThreshold("Otsu dark");
    run("Convert to Mask");
    run("Watershed");
    run("Analyze Particles...", "size=50-Infinity circularity=0.5-1.0 display summarize");
    close();
}