I have attached a sample pipeline that I made to convert segmented images into grayscale for subsequent analysis. I have attached 2 tif files that are colored images of segmented objects, taken at different planes within the same stack. I have saved them manually because I would like to be able to use these images in various pipelines, for example: to test a pipeline in development, to resegment them under a second set of conditions or to subtract one from the other to eliminate duplicate objects.
- When I try to use the images in a pipeline after converting them to grayscale, I get the error message:
There was a problem running the analysis module IdentifyPrimAutomatic which is number 04.
Image processing was canceled in the IdentifyPrimAutomatic module because it requires an input image that is two-dimensional (i.e. X vs Y), but the image loaded does not fit this requirement. This may be because the image is a color image.
CPretrieveimage in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CPsubfunctions\CPretrieveimage.m (72)
IdentifyPrimAutomatic in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\Modules\IdentifyPrimAutomatic.m (515)
AnalyzeImagesButton_Callback in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (10442)
gui_mainfcn in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (12182)
CellProfiler in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (57)
- I’ve had this problem in other programs as well when trying to work with masks or other overlays. What is the nature of these images? Do they have bit depth? Is there a way to convert them into a binary image that can be read on CellProfiler?
Thank you so much!
ColorToGray_for_reanalysisPIPE_JML.mat (1.04 KB)