Coloc. Tools Tab

Tool Bar

Only visible if Show All is activated.

Displays tools to draw regions for analysis into the image. For a description of the individual tools, see Graphics Tab.

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ROI

Only visible if you have drawn a region into the scatter plot.

As long as this button is activated (highlighted in blue), you can select, move and change the regions in the scatter plot. If you want to change the quadrant lines again, you need to deselect the button.

Channels

Selects which channels of a multichannel image are compared with one another. Select a channel for both the horizontal and vertical diagram axis. The first and second channel are always selected by default. As soon as you have made a selection, all other channels are automatically removed from the image display. You can, however, add other channels temporarily on the Dimensions tab.

Threshold

Sets the threshold value (in gray levels) for both channels using the two Threshold sliders and the two spin boxes/input fields.

Range

Only visible if Show All is activated.

Defines the grey value range displayed by the axes of the scatter diagram.. Auto is selected here by default, which means that the range is automatically set to the brightest pixel in the image. You can, however, enter a fixed gray value range between 256 (8 bits) and 65535 (16 bits).

Dimension Selection

Only visible if at least one of the Range dropdown lists is set to Auto and if the image is a z-stack or a time series. Defines whether the axis of the scatter plot is based on the values of the current image plane (2D), or on the entire z-stack (All Z)/time series (All T). In this way you can easily determine a valid diagram setting for an entire time series, for example, without having to analyze each individual time point.

Costes

Calculates the optimal threshold value according to Costes et al.

Regions

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Channel buttons

Here you can mask pixels in the image according to which one of the four quadrants they belong to. The numbers on the buttons correspond to the numbering of the quadrants in the X/Y scatter plot. The color selection window is accessed by clicking on the color field.

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Cut Mask

Only active if a quadrant has been masked.
Creates a new image exclusively containing the masked pixels.

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Opacity

Only visible if Show All is activated.

Define the degree of transparency of the masking.

Extract

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Scatter Plot

Creates a new image document from the X/Y scatter plot. In the case of time series or z-stacks, the dimensions are also created automatically.

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Table

Only visible if Show All is activated.

Creates a new table document. The document contains all measurement data from the colocalization analysis. All dimensions, such as T and Z, are also taken into account. This table can be saved as a *.csv document for further processing in other programs.

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Table

Only visible if Show All is activated.

Activated: Displays the colocalization table in the image area.