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PathcoreScholar User Manual

Image Settings


The Image Settings panel can be used to alter the rendering of multi-channel images in the Viewer.

Sub-images

Some image files may contain multiple fields of view spanning a larger scan area (like a collage). These image files are more complex than traditional WSI because a file contains multiple images (a.k.a. sub-images), each of which may have different scanning properties.

While the Viewer treats each file as a single image, it allows the user to configure some of the properties of sub-images independently (e.g., focal plane and render settings).

If an image file contains sub-images that are separated by empty space (i.e., areas that are not scanned), the background color is automatically chosen, often to match the approach in the image vendor's native viewer.

The Viewer seamlessly handles overlapping sub-images and allows the highest available magnification to be used across all sub-images.

To adjust the visibility of sub-images

  1. From within the Viewer, click on the Layers button at the bottom left of the Viewer to reveal the Image Settings dialog

  2. Click on the Eye icon to toggle the visibility of any sub-image

  3. Close the Image Settings dialog by clicking on the X button at the top right corner of the popup dialog

Sub-images can be distinguished from image channels because all sub-images have the same name as the image file itself.

Channel Visibility

The visibility of each channel for non-RGB images or sub-images can be controlled independently. Once these settings are adjusted, they will be saved as preferences for the currently logged-in user.

To adjust the visibility of an image channel

  1. From within the Viewer, click on the Layers button at the bottom left of the Viewer to reveal the Image Settings dialog

  2. Click on the Eye icon to toggle the visibility of any channel

  3. Close the Image Settings dialog by clicking on the X button at the top right corner of the popup dialog

Sub-images can be distinguished from image channels because all sub-images have the same name as the image file itself.

Channel Color Corrections

There are a number of color correction options available that can be used to alter how a multi-channel image renders on-screen. The values that are shown by default are obtained from the image file itself, if available. Once these settings are adjusted, they will be saved as preferences for the currently logged-in user.

Color correction cannot be used on interlaced pixel types (e.g., RGB pixel type commonly used for brightfield images).

The channels for each sub-image can be adjusted independently.

Pseudocolor

The default color of each channel can be modified to any RGB value.

To change the pseudocolor of a channel

  1. From within the Viewer, click on the Layers button at the bottom left of the Viewer to reveal the Image Settings dialog

  2. Click on the colored square next to the channel name to open the color palette

  3. Select a color in the palette

  4. Close the Image Settings dialog by clicking on the X button at the top right corner of the popup dialog

To reset the pseudocolor of a channel to its default value

  1. From within the Viewer, click on the Layers button at the bottom left of the Viewer to reveal the Image Settings dialog

  2. Click on the Undo button next to the channel name

  3. Close the Image Settings dialog by clicking on the X button at the top right corner of the popup dialog

Histogram Corrections

Though the histogram is not visible, its properties for each image channel can be adjusted using the following parameters:

  • White Point, in the range [0.0, 1.0], is the saturation point on the RHS of the histogram
  • Black Point, in the range [0.0, 1.0], is the saturation point on the LHS of the histogram
  • Gamma, in the range [-2.0, 2.0], is the gamma correction factor
To adjust the histogram

  1. From within the Viewer, click on the Layers button at the bottom left of the Viewer to reveal the Image Settings dialog

  2. Click on the channel name to open a panel of sliders

  3. Adjust any of the sliders

  4. Close the Image Settings dialog by clicking on the X button at the top right corner of the popup dialog

To reset the histogram to its default value

  1. From within the Viewer, click on the Layers button at the bottom left of the Viewer to reveal the Image Settings dialog

  2. Click on the channel name to open a panel of sliders

  3. Click on the Undo button next to any of the histogram values

  4. Close the Image Settings dialog by clicking on the X button at the top right corner of the popup dialog

Auto Scale

The "Auto Scale" feature automatically configures the black and white points of multi-spectral images based on the dynamic range of each channel. This can be used to improve contrast and establish baseline values for the black and white points quickly.

This feature is only available for multi-spectral images.
To automatically configure black and white points for a single channel

  1. From within the Viewer, click on the Layers button at the bottom left of the Viewer to reveal the Image Settings dialog

  2. Click on the channel name to open a panel of sliders

  3. Click on the Auto Scale button below the sliders

  4. Close the Image Settings dialog by clicking on the X button at the top right corner of the popup dialog

To automatically configure black and white points for all channels

  1. From within the Viewer, click on the Layers button at the bottom left of the Viewer to reveal the Image Settings dialog

  2. Click on the Auto Scale button at the bottom of the dialog

  3. Close the Image Settings dialog by clicking on the X button at the top right corner of the popup dialog

To reset all black and white points to their default values

  1. From within the Viewer, click on the Layers button at the bottom left of the Viewer to reveal the Image Settings dialog

  2. Click on the Reset Scale button at the bottom of the dialog

  3. Close the Image Settings dialog by clicking on the X button at the top right corner of the popup dialog