Enhanced CellClassifier remains in the "Save-Mode". In order to start, Enhanced CellClassifier is missing data from a CellProfiler output file. Use >> File >> Merge and split data, to bring the output file into the right format. Choose either >> File >> New Experiment or >> Settings >> Modify Settings followed by the "Browse" button of the "Load data path" and select the _handles.mat file of the newly split data.
No original images are available. Choose either >>à File >> New Experiment or >> Settings >> Modify Settings. Use the "Browse" button of the "Load original images path" and select the appropriate folder. Alternatively press "LUCKY" for an automatic selection.
Possiblity 1: No Segmented images are available. Either no segmented images exist or the path is incorrect. For selection of objects on the images, CC needs Segmented Images (=LabelMatrixImages). These images indicate the borders (segmentation) of the objects. You need to create these images with CellProfiler (module: ConvertToImage, option 'uint16', and module: SaveImages as 'mat' file).
Select the path to the segmented images either in >> File >> New Experiment or >> Settings >> Modify Settings.
Possiblity 2: Segmented images exist in the correct folder but cannot be recognized by Enhanced CellClassifier. The filenames for the segmented images are generated by replacing string 1 by string 2 in an image-filename (for instance, replacing '.tif' by '.mat'). You can adjust these strings in the "Define Settings" window.
Possibility 3: No data are selected. You can select the data that will be used for classification in the "Define Settings" window (>> Settings, >> Modify Settings). Press the "+" button to add a new measurement. Make sure, that only objects which necessarily have the same number in each image are combined (for instance 'Nuclei' and 'Cells', when each cell is generated from a nucleus).
LIBSVM is incorporated in the Enhanced CellClassifier program. It needs .mex files (C++ files which are Matlab-executable) to work. .mex files might be different for different environments (32-bit windows, 64-bit windows, Macintosh, etc.). Enhanced CellClassifier checks, whether the respective files for the current environment are there, if not, the SVM-window does not open.
The .mex files for 32-bit windows, 64-bit windows, and MacIntel are already there. If you are working in a different environment, you might need to make these files yourself. Please read the instructions in the "readme" file, in the LIBSVM-folder in the Enhanced CellClassifier program and act accordingly.
For Macintosh the following strategy worked (thanks Micha):
If all this does not work, contact LIBSVM (or us) for technical support. http://www.csie.ntu.edu.tw/~cjlin/libsvm/
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