Preferences: Images

Open

These options are used when BrainMaker opens images, but cannot identify their bit depth.

When a high bit depth (greater than 8) image is loaded, the display may not be optimal for visualization because the image contains a broad range of values (e.g., 65,536 values for a 16-bit image) while the monitor is only set to display up to 256 values (8-bit depth range). As a result, BrainMaker software maps the pixel range into a smaller color intensity range.

In addition, the pixel values in the image file are typically expressed in 16-bit values although the image may have been generated by a 12 or 14-bit camera. As a result, some of the bits in the image may be expressed as 0.

Bit depth affects only the display of images, not the underlying data.

Use max pixel

BrainMaker software selects the lowest bit depth that includes the highest pixel value found within the image.

Example: If the highest pixel value found in the image is 3965, then the minimum bit depth that could include this value is 12 since the range for a 12-bit image is 0-4096. Neurolucida will use 12 as the bit depth.

12 may not be the actual bit depth range of the image (i.e., the image could have been created in a 16-bit image space), but the maximal pixel value contained with that image is still 3965.

Use “x” bits per pixel

If you know the full bit-depth range for the image, select it from the drop-down menu.

Always Ask

When selected, the Unknown Bit Depth window is displayed when opening the image.

White Point

By setting the white point (i.e., the value associated with the white color), you can refine the range of values to be mapped for the display.

  • Maximum allowed by bit depth: The white point is associated with the maximal value of the range.

    Example: If you selected 12 as the bit depth, the white point is associated with 4095 and the range is 0-4096.

  • Maximum pixel of image(s): BrainMaker software identifies the maximum pixel value in the image and associates it with the white point. Doesn't depend on bit depth and may result in a narrower range than the bit depth range.

    Example: If 12 is the bit depth, the white point might be associated with 3200, which is lower than the maximum pixel value for a 12 bit depth (4096). 3200 is used as the white point value.

Black Point

By setting the black point (i.e., the value associated with the black color), you can refine the range of values to be mapped for the display.

  • 0 (Min. allowed by bit depth): The black point is associated with the minimal value of the range, which is 0.

  • Minimum pixel of image(s): BrainMaker software identifies the minimum pixel value in the image and associates it with the black point. This does not depend on bit depth.

    Example: The minimal pixel value is identified as 120 (instead of 0). 120 is used as the black point value.

  • When selected, the image and/or tracing is automatically sized to fill the window while preserving the aspect ratio.
  • When unchecked, the image and/or tracing is displayed using the reference point as the origin.

By default, the program only displays the Image Scaling dialog when it cannot identify scaling. Also see Image scaling dialog.

View

Select when working with single-channel images requiring false coloring.

If left unchecked, image stacks are loaded with the first image at the current Z position, with the images in the stack placed at regular intervals in Z from the first image.

Useful to identify the current image.

Alternative method: Use the Image Organizer; the current image is identified by a blue highlight for the image information.

Displays the Image File Reader Channel Colors dialog box.

Use with multichannel image files that don't contain color specifications (e.g., Nikon IDS/ICS files) to assign colors to display.

When checked, the acquired and imported image thumbnails are shown in their appropriate locations in Where Is mode.

Affects the viewing of Image Processing effects. If this option is checked, the preview area will disappear after an Image Processing effect has been applied. It can be turned back on by checking the Preview box in the Image Processing dialog box.

This option affects the viewing of Image Processing. If this option is checked, a preview window automatically appears whenever a new image Processing effect is selected.

Acquires "n" images and averages these "n" acquisitions into a single image. Use this option if your camera generates a lot of noise in the image.

Number of images to use: Start with a small number and gradually increase until the noise reduction is satisfactory.

Save

Select to automatically save the acquired images to a defined path.

Optional: Use a base name. As each image is saved, the program uses the base name and a number that increments by 1.

Use this option to use configuration files separate from image files. MBF-specific information includes data about the Data DIB, Display DIB, and other information about the image file and how the program should process it.

Use this option to use configuration files separate from image files. Adjustments are saved in a separate file to avoid modifying the image.