BodenmillerGroup/ImcSegmentationPipeline: Restructuring the pipeline

The pipeline was adjusted to address some of the open issues. In detail the changes can be seen in [https://github.com/BodenmillerGroup/ImcSegmentationPipeline/blob/main/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 probabilitie