The View Settings Panel
The View Settings panel gives basic tools for visualization of the dataset.
This table contains a list of color channels of the dataset. The color channels may be switched on and off (a combination of Ctrl+left mouse click above checkboxes turns on selection of a single color channel). The image is generated depending on selection state of the LUT checkbox. When the LUT checkbox is selected im_browser generates the final image based on defined colors (the third column in this table). Note! When the LUT checkbox is unchecked the maximal number of colors that can be shown simultaneously is limited to 3. If more than 3 colors are selected then only the first 3 color channels are shown.
The right mouse button gives access to additional color channel actions:
- Insert empty channel..., insert an empty channel (intensity of all pixels is 0) to the specified position
- Copy channel, to copy the selected color channel to a new channel (available also from Menu-Image-Color Channels)
- Invert channel, to invert the selected color channel (available also from Menu-Image-Color Channels)
- Rotate channel, rotate the specified color channel (available also from Menu-Image-Color Channels)
- Swap channels, to swap the selected color channel with another one (available also from Menu-Image-Color Channels)
- Delete channel, to delete the selected color channel (available also from Menu-Image-Color Channels)
- Set LUT color, to set colors for use with the LUT checkbox (available also from Menu-File-Preferences)
A brief demonstration of work with color channels is available in the following video:
Switch on/off the Model layer. This check box has a shortcut 'spacebar'.
Switch on/off Mask layer. This check box has a shortcut 'Ctrl + spacebar'.
Switch on/off display of the Image layer.
Switch on/off Annotation layer.
Press to start display adjustments GUI tool, see more here.
The Auto button Auto brightness adjustment of complete dataset. The function asks for saturation parameters for both low and high intensity borders. As a result, the image intensities are recalculated to increase the contrast. Note, the function behaviour is affected by the stack switch. When the stack switch is off the brightness is individually adjusted for each frame of the dataset. Alternatively, when checked, the function first finds minimal and maximal stretching parameters for the whole dataset and then uses these values to adjust the contrast.
The Contrast button Allows changing of the contrast of the image. Possible combinations:
- Left mouse click, contrast adjustment with desired parameters for the current frame or for the whole dataset. Note! It is better to use Display (6.) button for contrast adjustment.
- Right mouse click + Show histogram, shows histogram of the current image in a separate window to find best parameters for contrast stretch.
- Right mouse click + Contrast-limited adaptive histogram equalization, starts Contrast-limited adaptive histogram equalization (CLAHE) for the choosen part of the dataset. See help for adapthisteq Matlab function for details. This option is also available from the Menu->Image->Contrast.
The on fly checkbox automatically adjust contrast for each shown image without recalculation of intensities of the actual data.
- The top trasparency slider regulates transparency of the Model layer from opaque (slider in the left position) to transparent (slider in the right position). For the difference maps (result of the correlation analysis) this slider changes the gain of the difference map.
- The middle transparency slider changes transparency values for the Mask layers from opaque to transparent.
- The lower trasparency slider change transparency values for the Selection layer from opaque to transparent.