Choose Fiji or ImageJ when
Use Fiji or ImageJ when the workflow depends on open-source processing, scripting, custom plugins, batch macros, or a method already validated in your lab. SlideScope now handles standard nuclei, cell and particle segmentation and counting with a saved recipe, but it has no macro language and does not author custom pipelines, so it complements that ecosystem rather than replacing it.
Where the other analysis tools fit
Fiji and ImageJ are not the only tools people weigh here. If the job is a repeatable measurement pipeline across many images, compare CellProfiler instead. If it is whole slide object detection or Python-native work, compare QuPath and napari. The microscopy image analysis software page maps where viewing, calibrated measurement, and quantification each belong.
Non-affiliation note
SlideScope is independent and is not affiliated with Fiji or ImageJ. Product names are used only to describe comparison and alternative search intent.