![cellprofiler output during processing cellprofiler output during processing](https://image2.slideserve.com/4815488/data-export-modules1-l.jpg)
The MeasureTexture module now allows users to explicitly select how many gray levels they wish to measure their images at- CellProfiler 2 used 8, CellProfiler 3 used 256. Users concerned about processing speed may wish to disable running Costes measurements in the module settings. This has now been corrected, but these statistics can be computationally expensive on high bit depth images. This could produce invalid results when working with 16-bit images. The MeasureColocalization module previously assumed that input images were in 8-bit format when performing Costes measurements. This can produce slightly different results. The MeasureObjectSizeShape module now uses the scikit-image implementation for most measurements. This will impact the Threshold, IdentifyPrimaryObjects and IdentifySecondaryObjects modules. In general, many of the libraries we use have updated their thresholding implementations, so thresholding settings on all upgraded pipelines should be checked and adjusted before use. The 3-Class Otsu thresholding method was calculated incorrectly in some situations and has now been fixed.
![cellprofiler output during processing cellprofiler output during processing](https://image2.slideserve.com/4815488/data-export-modules-l.jpg)
![cellprofiler output during processing cellprofiler output during processing](https://www.biorxiv.org/content/biorxiv/early/2020/05/16/2020.05.15.093369/F10.large.jpg)
Key points to take note of are as follows:
#Cellprofiler output during processing code#
This has involved extensive restructuring of the code base, leading to a lot of “under-the-hood” improvements.Īs a major release, this version contains changes to CellProfiler that will alter the behaviour of pipelines from previous versions of the software. The primary goal of this release has been to migrate CellProfiler from Python 2 to Python 3. We have now released CellProfiler version 4.0! Download it here.