Restructuring the pipeline

The pipeline was adjusted to address some of the open issues. In detail the changes can be seen in CHANGELOG.md and include:

• replaced imctools by internal imcsegpipe package calling readimc
• adjusted the pre-processing script in terms of function calls and documentation
• added script to download raw IMC data from zenodo.org/record/5949116 and the ilastik pixel classifier from zenodo.org/record/6043544
• moved the hot pixel filtering step from the CellProfiler pipelines into the create_analysis_stacks function call
• removed the default tiffs folder. All files related to ilastik pixel classification are stored in the ilastik folder and image crops are stored in crops
• hot pixel filtered images are directly written out to cpout/images
• segmentation masks are directly written out to cpout/masks in the second pipeline and read in as objects in the last pipeline
• pixel probabilities are downscaled in the second pipeline and directly written into cpout/probabilites
• cell segmentation is performed on downscaled pixel probabilities