Fixes wrong naming in compensate Measurements

This release fixes a bug in the CorrectSpilloverMeasurements module that caused the name suffix to be appended to the Image instead of the Measurement feature name.

This also includes the following changes:

• Adds a new ExportVarCsv module: This module parses measurement names from output tables into a clean metadata file that should facilitate the import of cellprofiler output into data structures such as anndata.

CP4 release: fix docstring error

Due to an issue with the two documentation strings, the two 'measure multichannel' modules did not load correctly in the v4.0 release.
This is now fixed.

First CP4 release

This is the official update to the modules to Cellprofiler 4.

Changenotes:

• Modules should not have changed functionality and old pipelines should load fine.
• Some modules have been deprecated (see README) or renamed (removing spaces in module name). Please read the deprecation notes displayed when loading a pipeline with such modules.
• Modules which can be adapted automatically (e.g. renamed modules) should adapt automatically when opening and saving a pipeline with CP4.
• Added more tests and documentation.

Please let me know if there are any issues!

Final CP3 release

This is the final release before upgrading the plugins to CP4.

Changelog:

• Made image cropping parametric: now it is possible to add a seed depending on a string or on user provided metadata to make random crops reproducible. If metadata is used (right click into string field), this allows to reproducibly crop for images that have the same metadata.

Bugfixes and new modules

New modules:

• 'ClipRange' module to clip the intensity range using a percentile (#34 )
• StackImages module: allows to stack single plane and multiplane images (#29)

New features:

• 'SmoothMultichannel': add the median filter from scipy (#33)

Fixes:

• The ObjectCrops module is now CP3 compatible (#35)
• Compensation works now also when some measurements are NAN (#26)

Updated CP3 plugins

This releases the latest changes in the CellProfiler 3 plugins.

The issues addressed are:

• All modules should now be CP 3.1.5 compatible
• Issue #19: Indexing for channels in measureimages and measureobjects was different -> now it is 1 based indexing
• Faster image smoothing using smooth multichannel
• Adds a saveimages_h5 module to allow saving images in a Ilastik compatible hdf5 format -> Allows to pass images directly to ilastik without requiring the tifffile library installed as before.
• Updates README

Please open issues if you find any problems!

IMC data related plugins for CellProfiller 2

These plugins are used in the CellProfiler and Ilastik based multiplexed image segmentation pipeline developed and used in the Bodenmiller lab:
https://github.com/BodenmillerGroup/ImcSegmentationPipeline

To install unzip the folder and point your Cellprofiller settings to the 'plugins' subfolder.

BETA: IMC data related plugins for CellProfiller 3

These plugins are used in the CellProfiler and Ilastik based multiplexed image segmentation pipeline developed and used in the Bodenmiller lab:
https://github.com/BodenmillerGroup/ImcSegmentationPipeline

To install unzip the folder and point your Cellprofiller settings to the 'plugins' subfolder.