ImageJ

Counting Cells with ImageJ

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• published: 11 Sep 2013
• views: 96666

Keep in mind that ImageJ processing is not perfect. However, the error of missing cells may be "corrected" by the error of including some noise. Steps in Video: Process - Subtract Background Image - Adjust - Threshold Process - Binary - Fill Holes Process - Binary - Convert to Mask Process - Binary - Watershed Analyze - Analyze Particles Basic description of tools: Subtract Background - cancel out noise of the background Threshold - change the image to binary image of red, black and white, or blue Fill Holes - fill empty spaces between rings to make circles Convert to Mask - allows for subsequent processing Watershed - automated separation of separate fused cells by a 1 pixel line Analyze Particles - process the image to acquire a cell count Size - parameter of what cells to include in data by area (pixels^2) Circularity - parameter of what cells to include by how close to a circle the shape appears. The maximum bound (1.0) means a perfect circle. The minimum bound deviates from being a circle. Show - Outlines will trace the outside of the mask images. Masks will show the black and white image similar during thresholding. Exclude Edges - ImageJ will not include cells that are not fully contained in the boundaries of the image Macro Code: run("Subtract Background...", "rolling=12"); setAutoThreshold("Default dark"); setThreshold(35, 255); run("Convert to Mask"); run("Fill Holes"); run("Convert to Mask"); run("Watershed"); run("Analyze Particles...", "size=120-Infinity circularity=0.00-1.00 show=Outlines display exclude clear summarize");