Look for up to 5 cells that are clearly misclassified. On Macs, select “View” from the image menu, and then select “View cell classes as numbers.” Then, to see what each number means, click the “Show controls >” button at the bottom to
#Cellprofiler vs cellprofiler analyst windows
On Windows computers this will also show which color corresponds to which class. Click the “Show controls >” button at the bottom to reveal the total counts of each class on the The cells will be color-coded according to their classification based on the current rules. The cells will be color-coded according to their classification based on the current rules.įrom the image that opens, click “Classify” from the menu, then “Classify Image”. From the image that opens, click “Classify” from the menu, then “Classify Image”. Double-click any of cell thumbnails in the positive or negative bins. You may also apply the rules to all the identified cells in an image, and use it to correct misclassifications.
Refining the training set by correcting misclassified cells in an image:
Divide the "MeanIntensity" of the rawGFP intensity from the nuclei by the of the cytoplasm. Select "Divide" from the drop-down for the "Operation" setting. Type "IntensityRatio" as descriptive name for the output measurement. Measurement of the ratio of GFP in cytoplasm to GFP in nuclei: Add the CalculateMath module.For the select where to measure correlation setting, select "within objects" and then select "Nuclei" and "Cytoplasm" from the "Select objects to measure box". Leve the "Set threshold as percentage of maximum intensity for the images to the default value of 15.0. Select "rawGFP" and "rawDNA" from the Select images to measure box. Measurement of the correlation of GFP in nuclei and DNA in nuclei: Add the MeasureColocalization module.Select "Cytoplasm" and "Nuclei" under select objects to measure. Select "rawGFP" under select images to measure. Measurement of pixel intensity of GFP in nuclei and cytoplasm: Add the MeasureObjectIntensity module.Measure the cells' characteristics ("object features")
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