I am trying to use CellProfiler v2 to measure fluorescence intensity from neurons of different regions of rat hippocampus acquired as a whole montage.
My work flow is as follows:-
I have created masks (created as gray scale) for different regions of hippocampus using Photoshop.
- Load the image montage to CP.
- Resize the image
- Load the mask for the region of interest and convert to binary using ApplyThreshold
- Identify primary objects (nuclei) , secondary objects (cells) and tertiary objects (cytoplasm).
- Measure object intensity and object shape.
- Save image and export to spreadsheet.
However, when I try to run it by clicking ‘analyze images’, or run in the test mode, I get the following error message and the pipeline stalls.
Traceback (most recent call last):
File “cellprofiler\gui\pipelinecontroller.pyc”, line 932, in do_step
File “cellprofiler\modules\loadimages.pyc”, line 2074, in run
File “cellprofiler\modules\loadimages.pyc”, line 2781, in provide_image
File “cellprofiler\cpimage.pyc”, line 84, in init
File “cellprofiler\cpimage.pyc”, line 142, in set_image
i am also attaching the pipeline and the images for your reference.
How can I make it work? I will be grateful for any of your suggestions.
NKCC1 Rev.1 For Testing.cp (179 KB)