I – File Selection

Well group radio buttons

Lower right of the image. CellProfiler allows predefining 4 different well groups. "all" includes all wells and is always present. A useful pre-selection might be:

• Positive expected: where the majority of the objects has a positive phenotype, (Class 1 phenotype)
• Negative expected: where the majority of the objects has a negative phenotype (Class 2 phenotype)
• Mixture: which should be a representative mixture to be analyzed
• Special: objects which a special phenotype, for instance a borderline phenotype.

The well groups and the names on the buttons can be defined in the "Define Settings" windos. When pressing one of the radio buttons, a new image is selected from the respective well group, WITHOUT saving the objects trained in the current cycle (pressing the radio button again equals to "Save Data" without saving, which can also be useful because it is a browsing option through the images).

Blind

Normally the filename of the current image is displayed. However, this might cause a training bias because the setup of the plate is usually known to the user. After checking "blind", the filename is replaced by a (well meaning) sentence.

Browser buttons

Next to the well group radio buttons:

>>

<<

Selects the next or the previous image, respectively.

Image Selection

>> Image Navigation >> Image Selection >> Random

>> Image Navigation >> Image Selection >> Random do not show image twice

>> Image Navigation >> Image Selection >> Next

>> Image Navigation >> Image Selection >> revious

Determines, how the image is selected after pressing "Save Data".

Either: randomly, or the next or previous image of the current image population (according to the well group radio buttons). If in the "next" or "previous" mode, the first or last image is reached, CC switches back to the "random" mode.

Default mode and recommended mode: "random" (to prevent any selection bias)

For the option "Random, do not show image twice", CC checks whether any object within an image contains any objects already trained. If this is the case, this image will not be shown again. This option is useful if the whole plate needs to be sampled.

Navigate to Specific Image

>> Image Navigation >> Navigate to Specific Image

A window appears which displays all available image files. This is the option to navigate to one specific image which might be of interest for whatever reasons.

Focus Exclusion

>> Focus >> Focus Exclusion >> Focus Exclusion ON

>> Focus >> Focus Exclusion >> Focus Exclusion OFF

If this Focus exclusion is activated, out of focus images will be ignored in the Enhanced CellClassifier "Main Window" and a new image will be loaded. Depending on the settings in the "DefineSettings" window, the out of focus image is displayed in a separate window or not. Moreover, if focus exclusion is activated, in the "Generate ExcelFile" window, data from the out of focus images will not be summarized.

Focus exclusion requires that the images have been measured by the MeasureImageGranularity module of CellProfiler. Details of the Focus-Algorithm and focus settings can be found in the description of the "Focus window" (see below).