Changelog

March 8, 2023 ยท View on GitHub

[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