Changelog

[3.6, 08-03-2023]

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

[3.5, 07-11-2022]

exclude hidden files from processing

[3.4, 02-06-2022]

removed tifffile version pinning

[3.3, 27-04-2022]

fixed tifffile version

[3.2]

sort channels by metal tag when creating the ilastik and full stacks

[3.1]

fixed git submodule issue
specified in documentation to restart CellProfiler after setting the plugins

[3.0]

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

[2.3]

Bugfixes: 1_prepare_ilastik: Removed special characters from pipeline comments as this caused encoding issues.

[2.1]

Bugfixes: 1_prepare_ilastik: Fix range to 0-1 for mean image, preventing out of range errors

[2.0]

Change to imctools v2: Changes the structure of the folder to the new format, changing the naming of the .ome.tiff files
Change to Cellprofiler v4: Requires the use of the ImcPluginsCP master branch or a release > v.4.1
Updated documentation
Adds var_Cells.csv containing metadata for the measurements
Adds panel to cpout folder