Allow handling of MCD files with missing channel labels

• allow handling MCD files with missing channel label entries
• updated links to raw data on Zenodo
• switched from MCDFile.metadata to MCDFile.schema_xml to keep up with the latest version of readimc

Exclude hidden files from processing

Merge pull request #109 from BodenmillerGroup/hidden-files-bugfix

exclude dotfiles (closes #94)

Remove tifffile pinning

Relates to the xtiff fix in https://github.com/BodenmillerGroup/xtiff/releases/tag/v0.7.8

Fix tifffile version

Workaround for #90 and #92

Sort channels by metal tag

Revert back to original channel sorting

Adjustments to ensure functionality

The git submodules were fixed and docs were appended to indicate restarting of CellProfiler when setting the plugin directory.

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

Remove special characters from Pipelines

This bugfix fixes issue #66 and was contributed by @nilseling .

Special characters are removed from pipeline comments in 1_prepare_ilastik

Fix rescaling bug

This addresses issue #57 that was caused by average images calculated
for pixel classification potentially being outside of the allowed range.
Now all images are rescaled to the allowed value range.

The implementation was done such that backwards compatibility is preserved.

Cellprofiler 4 and `imctools v1` release

This release requires Cellprofiler 4 together with the ImcPluginsCP version > v4.2.1 (https://github.com/BodenmillerGroup/ImcPluginsCP/releases). Further, the example scripts rely on imctools v2.

Breaking changes:

• Imctools v2 changed the naming scheme of files - if you use this version you might need to adapt downstream scripts to the new file naming
  -> Due to the new naming scheme this also requires the re-conversion of .mcd folders to ome

This release adds the following improvements:

• Updated documentation
• Adds var_Cells.csv containing metadata for the measurements
• Adds panel to cpout folder