I am currently using CP for segmenting and tracking yeast cells. The segmentation works well for the fluorescent chanell by using the module IdentifyPrimAutomatic with the Otsu global thresholding methos and intensity as a method to distinguish clumped cells. This turned to be the best method for segmentation after optimization with all the parameters (diameter, threshold correcting factor, filter size,etc…). However, some of the cells split to 2 objects in some of the images along the movies and this interferes with the subsequent tracking algorithm. Do you have an idea how I can solve it?
Other questions are related to the tracking module:
- Can I run the tracking from the end of the movie to its begining, because the cells are dividing during the acquisition time?
- When I tried to export to excell I’ve got the following error message:
There was a problem running the image analysis. Sorry, it is unclear what the problem is. It would be wise to close the entire CellProfiler program in case something strange has happened to the settings. The output file may be unreliable as well. Matlab says the error is: Index exceeds matrix dimensions. in the ExportToExcel module, which is module #05 in the pipeline.
CPwritemeasurements in E:\Cellprofiler\CellProfiler_1.0.5122_MATLAB\CPsubfunctions\CPwritemeasurements.m (329)
ExportToExcel in E:\Cellprofiler\CellProfiler_1.0.5122_MATLAB\Modules\ExportToExcel.m (124)
AnalyzeImagesButton_Callback in E:\Cellprofiler\CellProfiler_1.0.5122_MATLAB\CellProfiler.m (3829)
gui_mainfcn in E:\Cellprofiler\CellProfiler_1.0.5122_MATLAB\CellProfiler.m (5575)
CellProfiler in E:\Cellprofiler\CellProfiler_1.0.5122_MATLAB\CellProfiler.m (53)
Do you know how to solve it?
Thanks in advance,