These two KNIME workflow solutions are similar: first one detects nuclei and spots inside the nuclei without taking care of surrounding regions, i.e. mitochondria. The second one provides the full solution including spots in mitochondria.

see section 2.4 for KNIME workflow. Section 2.3 is also available, using Fiji. 

Sample image: hela-cells.tif (674k x 3)

has function

The original paper [publication 1] describes a method to analyze mitochondrial morphology in 2D and 3D and is based on previous work of the authors [publication 2].