Use nuclear masks for spot filtration

[vreuter]

• napari becomes part of pipeline and the pipeline set of dependencies, since we want to save visualisation of nuclei and detected nuclear masks.
• dependency declarations (still to be declared in build.sbt) for #208
• visualising nuclear masks and using them for spot filtration (#241)
• visualising pre- and post-nuclei-filtration spot counts
• modularising test dependencies
• cleaning up overall dependencies
• removing unused code
• centralising more path definitions on ImageHandler for reference from various pipeline components, using ImageHandler as a communication interface
• adding drift correction for nuclei