Image Adjustment

Overview

The Image Adjustment panel enables you to change how the current image looks. You can save these adjustments with the image if you choose; you'll be prompted to decide when you close the file or exit the software.

In images that contain more than one color channel, you can also use this panel to select an individual color channel before tracing/detecting structures; to associate traced/detected structures.

Click the Adjust button on the Image or Workspace ribbon to open the Image Adjustment panel.

Histogram

The histogram shows both a bar graph of the image data and a line that represents how that data set is mapped into a display image.

  X-axis Y-axis
Image-data bar graph Pixel-intensity value Number of pixels
Mapping into display image Pixel-intensity value color value (black is 0, white is 255)

You can adjust image appearance by typing values into the boxes below the histogram or dragging the controls on the histogram:

  • Black point: (black triangle) The black point is the pixel intensity that defines the lower end of the intensity/color mapping range. In the histogram above, there are no pixels at the lower end of the X-axis, so it may improve image display to drag the black point to where the bar graph shows that image data are present:
  • Gamma: Drag the gamma control (or type into the box) to adjust color mapping intensity in a non-linear fashion. The effectively emphasizes either the darker (gamma ≤ 1) or lighter (gamma ≥ 1) pixels in the image.
  • White point: (white triangle) The white point defines the upper end of the intensity/color mapping range. Similarly to black point adjustment, you may want to drag the white point to where the upper pixel intensity value has image data associated with it.

Display

Ungroup Color Channels: Check the box to list each color channel in multi-color channel images and enable individual color channels to be selected and/or modified.

  • To display/hide a channel, click to check/clear its Display check box.
  • If you select a single color for display in images that contain more than one color channel, any structures that are traced or detected using Neurolucida 360 software will be assigned to that color channel.
  • Conversely, if all color channels or more than one color channel are selected for display, structures traced or detected will not be associated with a specific color channel.

Note that, for tracing/detecting structures in the 3D environment, it may be more convenient to use the Channel panel in the 3D environment window to select color channels for association with reconstructed structures.

Apply changes to stack: When the box is checked, changes are applied to each image in the image stack. When the box is cleared, changes are applied only to the current image.

Apply to images checked in Image Organizer: When the box is checked, changes are applied to all images in the Image Organizer selected with a check-mark.

You can display either Brightness and Contrast or Gain and Offset controls. To choose:

  • Click the Show Options button to show the Display Options panel.
  • In Display Options, next to Work with, click the button next to either Brightness/Contrast controls or Gain / Offset controls.

Buttons

Reset: Resets the image to its original settings up to the last save.

Default: Sets the Black Point to 0 and the White Point to the highest value available for the image type.

  • For an 8-bit image, the highest White Point value is 255.
  • For a 12-bit image, the highest White Point value is 4095.

Optimize: Sets the black and white points to the lowest and highest appropriate values, respectively.

Show Options / Hide Options: Click to show or hide Display and Optimization Options.

Display Options

Show Luminance: Check the box to calculate luminance from color images (when possible) and display it on the histogram. Note that this is only available if the channels are grouped.

Always ungroup Color Channels: Check the box to ungroup color channels when opening images.

Use Simple Color Pickers when selecting colors: Check the box to display a set of colors to choose from for the color channels. Clear the box to enable the selection of additional color choices.

Optimization Options

Optimize images of a stack individually: The default behavior is to apply image-optimization adjustments to the image stack as a whole. Check the box to optimize each image in the stack individually.

More: Click the More button to adjust the settings used for image optimization or reset them to the default values.

Saving image adjustments

Image Only Stack Command Also Required
  √ File>Save as>Image Stack>Stack  
√   File>Save as>Image  
  √ File>Save>Image Stack>Stack

Adjust Preferences: Images:

Under Save, check the boxes next to:

"When writing image files..."

"When saving only image display adjustments..."
√   File>Save>Image