ImageJ's built-in Process -> Find Maxima command can be used for many 2D counting-related tasks. For counting small, bright foci (dots), set Output type to be Point Selection. If too many points are detected, the number may be reduced using one or more of the following methods: Apply a filter to reduce noise, e.g. Process -> Filters -> Gaussian Blur... prior to running Find Maxima Set a minimum threshold with Image -> Adjust -> Threshold... prior to running Find Maxima, then use the Above lower threshold option within the dialog box Increase the Noise tolerance value (which effectively acts as a local threshold) The resulting point selection can be modified (points added/removed) by the Multi-Point tool. After the points are available, final measurements can be made using Analyze -> Measure.