Preferences: Images

Purpose

Use Images preferences to customize how images are opened, displayed, and saved in BrightSLICE.

Access Images preferences from File > Preferences > Images.

Open

Enable smart optimize for images with low signal: When enabled (checked), image display is automatically optimized if low signal is detected when opening files. Note that, if you're opening multiple image files, you can cancel the smart optimize operation by hitting the Esc key on your keyboard and choosing to cancel when prompted.

Zoom to fit on load: When enabled (checked), the image and/or tracing is automatically sized to fill the window while preserving the aspect ratio.

Load all stacks at same Z: 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 compared to the first image. Check the box to load all image stacks at the same Z position.

Show Image Scaling dialog on opening image: By default, BrightSLICE displays the Image Scaling dialog only when it cannot identify scaling. Check the box to display the dialog every time you open an image. This may be useful when:

  • You want to verify the image scaling values.

  • Images have been saved with inaccurate image scaling that needs to be corrected.

  • You want to use the image file scaling values to create a new software lens.

Enable resampling quality bias: This is an advanced feature that we recommend keeping disabled (unchecked) for the most part. Our Technical Services staff may recommend enabling it to increase the quality of image-data display. Enabling resampling quality bias, however, will decrease the speed of image loading.

View

Marquee around current 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.

When using PgUp/PgDown keys, restrict navigation to current stack in Image Organizer: Navigating up and down through the stack with the PgUp/PgDown keys on the keyboard will only apply to the image currently selected in the Image organizer.

Use F9-F12 to: Choose from the dropdown whether the F9-F12 keys on the keyboard select or toggle filter colors.

Save

Save images when they are acquired: 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.

Suppress warning for saving single image of a stack There are two image save options in the file menu, Save/ Save as image and Save/ Save as image stack . If save image is chosen, but an image stack, rather than a single-plane image is the active file, you will see a warning that continuing will save just the current plane of the image stack. Select this option to suppress the warning.

When writing image files, write MBF-specific data to external XMP file: Select to create an external XMP file when saving an image. This will modify the original image and also save scaling and display adjustment information to an external XMP file where you can easily view and edit the image specific metadata.

When saving only image display adjustments, write these adjustments to just the external XMP file so the image file is not modified: Use this option to save changes to an external XMP file only. No changes will be made to the original image file.

Note that if the XMP file is present in the same folder as the image, BrightSLICE will use the metadata contained in the XMP file when opening the image. If the XMP file is removed from the folder containing the image, BrightSLICE will use the metadata that is embedded in the image file.

Clean temporary files on save failure: When saving JPX stacks, temporary JP2 files for each image plane are created. By default, those temporary files are deleted regardless of whether the save succeeds or fails. Select this option to keep the temporary files if the save fails.

Enable image organizer metadata editing: Select to enable the ability to edit metadata directly in the Image organizer window.

Aspect ratio

After zoom operation...: Sometimes the shapes of objects displayed on the monitor don’t seem to be an accurate representation of their actual (or expected) shapes. The perceived inaccuracy depends on how much the aspect ratio of the image file varies from the aspect ratio of the display monitor.

  • Image: For most images, the option to use aspect ratio of currently selected Image results in a satisfactory representation of the objects. This is because the aspect ratio of the pixels in the image file and the aspect ratio of the pixels in the display monitor are very similar.

  • Lens: If there is a significant difference between the aspect ratio of the pixels in the image file and the aspect ratio of the pixels of the display monitor, the option to use aspect ratio of currently selected Image results in an image with seemingly distorted (stretched or compacted) objects in one dimension, for example with MRI images.

    To resolve the apparent image distortion, use the option to use aspect ratio of currently selected lens. If needed, create a software lens that matches the aspect ratio of your display (likely to be close to 1.0).

All measurements reported by the program are correct regardless of the option selected (and even if the image appears distorted) .