Institute of Microbiology

H - Display

Enhanced CellClassifier can display 3 channels of an image; these three channels are referred to as "channel 1", "channel 2" and "channel 3". Enhanced CellClassifier can display only channels that have been loaded into the CellProfiler pipeline (module LoadImages). The choice which channel will be 1, 2 or 3 is made by the user in the "Define Settings" window. The first channel should be the one carrying the most relevant optical information because it is shown in grey, enabling best visual perception. The second and third channel is shown in grey and red, respectively, and can easily be turned on and off.

Channel 2 on, Channel 3 on

Checkbox, middle of lower part of the image: turns the display of the second or third channel off.

The second channel can also be turned on or off with the menu:

>> Display >> Show Second Channel

Or with the keyboard (Ctrl-Q - on, Ctrl-W - off)

Maxima Channel 1, 2 and 3

Maxima channel 1 (Checkbox): Scales channel 1 to the maximum of channel 1.

Maxima channel 2 (Checkbox): Scales channel 2 to the maximum of channel 2.

Maxima channel 3 (Checkbox): Scales channel 2 to the maximum of channel 2.

In order to see the relevant details in the images, the images have to be scaled relative to their intensity in their channels. If "Maxima Channel" is checked, the brightest pixel in the channel will have the maximum intensity; all other pixels have less, according to their original intensity. Please note, that there is no gamma correction.

While this scaling always results in an at least somewhat useful display, the scaling and the display of the images can be quite variable because the brightest point of a channel can be very different in each image. Since the visual perception of the phenotype to be classified often depends on the scaling of the images, classification will also be variable.

If "Maxima Channel" is not checked, the slider becomes active. Now the user can choose the maximum of the channel for display. Move the slider or click on the slider to choose the best channel scaling. This scaling results in a more stabile display.

[Description of image scaling by the slider in more detail: CC collects the histograms of the intensities of the images already displayed. The slider uses a log10 scale to find the intensity for the …1%, 10%, 50%, 90%, 99%, 99.9%... brightest pixel, according to the slider position. This intensity is now used as the maximum. While the histogram might change within the first few images displayed, it quickly becomes stabile.]

Intensity of the display sliders

While the slider selects the maximum of the input image used for scaling, the absolute intensity of the display can be adjusted using:

>> Display >> Maximum Channels >> Maximum Intensity Channel 1 or

>> Display >> Maximum Channels >> Maximum Intensity Channel 2

The maximum for the display of channel 3 can only be changed in the "Define Settings" window. This allows relative adjustment of the intensities of channel 1 versus 2 or 3 or a dimming of all channels. The valid ranges are between >0 (black) and 0.79 (white) for channel 1 and between >0 (black) and 0.79 (green or red) for channels 2 and 3, respectively.

Mark Objects (Rectangle vs. Outlines)

>> Display >> Mark Objects >> Rectangle (Ctrl-R)

>> Display >> Mark Objects >> Outlines (Ctrl-T)

The trained objects are by default marked with outlines. If the objects are small relative to the outlines, a significant part of the object might be hidden, making training harder. In that case, the objects should be marked with a rectangle (the smallest rectangle where the shape of the objects fits in will be calculated). You can define the distance of the rectangle to the object in the settings file.

Show all objects (shadows, outlines, rectangle, off)

>> Display >> Show all objects >> Show all objects as shadows (Ctrl-V)

>> Display >> Show all objects >> Show all objects as white outlines (Ctrl-N)

>> Display >> Show all objects  >> Show all objects as white rectangle (Ctrl-B)

>> Display >> Show all objects >> Show all objects as off (Ctrl-M)

To quickly understand, which objects have been recognized in the image, CC offers several possibilities. If some objects have not been recognized or if the outlines are not correct, modify the CellProfiler image analysis parameters.

Briefly clean

>> Display >> Briefly show clean picture (Ctrl-U)

Sometimes it might be desirable to quickly have an undisturbed look just at the picture without any outlines of classified cells. "Briefly clean" just achieves that. The option is deactivated after selecting the menu point again or simply after clicking on the image.


Zoom + : Zoom-In. The image is enlarged by 30%. The image now cannot be displayed in one piece. Therefore the sliders on the right and below of the image become active.

Zoom - : Only active after Zoom +. Decreases size of the image by 30%. If the original size is reached again, Zoom - and the sliders becomes inactive.


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© 2015 Microbiology ETH Zürich | Imprint | Disclaimer | 23 December 2009