Update the Readme for all CP3 changes

Corrects minor mistakes in the readme.

README.rst

@@ -9,28 +9,28 @@ handling, processing as well as measurement of multiplexed data. It was primaril
 written with imaging mass cytometry (IMC) data for a Ilastik based image segmentation workflow.
 Many modules are slightly modified versions of CellProfiler modules (https://github.com/CellProfiler/CellProfiler).
 
-The modules were tested with CellProfiler 3, however they are still to be considered BETA versions.
+The modules were tested with CellProfiler 3.
 
 For installation copy the folder to a local directry and modify the CellProfiler preferences to the plugin folder.
-
-Note that some plugins (save_object_crops and saveimages_ilastik) directly depend on the TiffFile python library for writing out tiff images.
-Please install the library on the CellProfiler associated python using:
-'pip install tifffile'
-
+
 The modules
 -------------------
 
 * ColorToGray bb: a slight modification of the 'ColorToGray' CP module to support up to 60 channels per image
+  -> This bill be deprecated as the corresponding change was pushed upstream to CellProfiller and should thus become available per default in the next version: https://github.com/CellProfiler/CellProfiler/pull/3619
 * Crop bb: Crop a specified or random location from the image
 * MaskToBinstack: allows to identify a main object in a mask and generate a stack of binary planes containing: 'is_maninobject', 'is_any_other_object', 'is_background'
 * MeasureImageIntensityMultichannel: Allows to measure all the image planes of a multicolor image 
 * MeasureObjectIntensityMultichannel: Allows to measure all the image planes of a multicolor image in objects 
 * Rescale objects: Rescales object segmentation masks
 * Save object crops: Crops object regions out of an image. One region per object.
-* Save images ilastik: a helper module to save images in a way that ilastik 1.2.1 will recognize it as xyc image -> relies on the TIFFFILE library!
+* Save images ilastik: a helper module to save images as `.tiff` in a way that ilastik 1.2.1 will recognize it as xyc image 
+  -> This will be deprecated, as I recommend to use the `saveimages_h5` module for this task and use `hdf5` instead of tiff
+  -> This module relies on the TIFFFILE library, that needs to be installed in the python that `cellprofiller` is using. 
 * Smooth Multichannel: allows to apply image filters to all stacks of a multichannel image
 * Sumarize stack: converts a multichannel image into a single channel image by applying summarizing functions, e.g. sum of all channels 
 * Transform binary: converts a boolean image to the 'distance to the border' between regions.
-* Correct Spillover apply: applies spillover compensation on the images. Requires a spillover tiff image (flaot image with dimensions p*p (p=number of color channels). This can e.g. be calculated witht he R software CATALYST for mass cytometry data (https://bioconductor.org/packages/release/bioc/html/CATALYST.html)
+* Correct Spillover apply: applies spillover compensation on the images. Requires a spillover tiff image (flaot image with dimensions p*p (p=number of color channels). This can e.g. be calculated witht he R software CATALYST for mass cytometry data (https://bioconductor.org/packages/release/bioc/html/CATALYST.html, example script: https://github.com/BodenmillerGroup/cyTOFcompensation/blob/master/scripts/imc_adaptsm.Rmd)
+* CorrectSpilloverApply:  applies spillover compensation on measurements, which is more accurate than on images (as object measurements are more accurate). Requires a spillover tiff image (flaot image with dimensions p*p (p=number of color channels). This can e.g. be calculated witht he R software CATALYST for mass cytometry data (https://bioconductor.org/packages/release/bioc/html/CATALYST.html, example script: https://github.com/BodenmillerGroup/cyTOFcompensation/blob/master/scripts/imc_adaptsm.Rmd)
 
 Pleas read also the documetation within CellProfiler for more hints how to use these modules!