classify image pixels as belonging to different classes using the machine-learning tool, ilastik.
ClassifyPixels performs per-pixel classification using the ilastik application. Ilastik is now bundled with the CellProfiler distribution; it applies supervised machine learning techniques to images to learn their features. A user trains a classifier with Ilastik and then saves the classifier. The user then uses the ClassifyPixels module to classify the pixels in an image.
ClassifyPixels produces an "image" consisting of probabilities that the pixel belongs to the chosen class; this image is similar to an intensity image that would be produced by fluorescence imaging. Provided that the classifier is sufficiently accurate, the image is well-suited for input into one of the Identify modules for object detection. More instructions on using the interface may be found here. Please note that you must use the same image format for classification as for the initial learning phase.
Currently, ilastik is only available for Windows, and is accessible from in the CellProfiler folder under the Start Menu. A 64-bit system is recommended for running ilastik.
Classifier file location
Select the folder containing the classifier file to be loaded.
You can choose among the following options which are common to all file input/output
- Default Input Folder: Use the default input folder.
- Default Output Folder: Use from the default output folder.
- Elsewhere...: Use a particular folder you specify.
- Default input directory sub-folder: Enter the name of a subfolder of
the default input folder or a path that starts from the default input folder.
- Default output directory sub-folder: Enter the name of a subfolder of
the default output folder or a path that starts from the default output folder.
Elsewhere and the two sub-folder options all require you to enter an additional
path name. You can use an absolute path (such as "C:\imagedir\image.tif" on a PC) or a
relative path to specify the file location relative to a directory):
- Use one period to represent the current directory. For example, if you choose
Default Input Folder sub-folder, you can enter "./MyFiles" to look in a
folder called "MyFiles" that is contained within the Default Input Folder.
- Use two periods ".." to move up one folder level. For example, if you choose
Default Input Folder sub-folder, you can enter "../MyFolder" to look in a
folder called "MyFolder" at the same level as the Default Input Folder.
Classfier file name
This is the name of the Classfier file.
Select the class
Select the class you want to use. The class number
corresponds to the label-class in ilastik