Semi-automated

This is a plugin bundled with native ImageJ.

See IJ reference for more details > Link

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis.

This method was originally designed to track objects (not necessarily spots) already identified in 2D 
frames and has been applied previously to particle tracking and analysis in high-speed atomic force microscopy image series.

An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks