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Counting Cells with ImageJ

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");