Opening and viewing image stacks

Purpose

The Image Stack module enables you to focus through an image stack in real time. BrightSLICE automatically keeps track of depth (Z-axis) values .

View the list of file formats/types compatible BrightSLICE and other MBF Bioscience software (PDF).

See Acquire an image stack for instructions on how to acquire image stacks using MBF Bioscience software/hardware.

What are image stacks?

An image stack combines multiple images into a single image file or collection.
The images that make up a single stack can be stored in a single multi-image file or in individual files.

Generally, we recommend

Image scaling

Image stacks may contain scaling information that BrightSLICE uses to determine the distance between image planes.
If your stacks don't have scaling information, you can manually enter it using the Image Scaling dialog box.

Opening image stacks

About image scaling

Image stack files may include scaling information (i.e., the µm to voxel ratio and the distance between image planes in the Z orientation). If files do not contain scaling information or BrightSLICE cannot interpret the embedded scaling information, the Image Scaling dialog is displayed.

Learn more about manually enter scaling information using the Image Scaling dialog box.

Drag and drop

Perhaps the easiest way to open an image stack is to simply drag and drop the file(s) onto the BrightSLICE software window using Windows explorer. Depending on the file(s), a dialog may open for you to enter additional information about how you want BrightSLICE to handle the file(s).

Open a single image stack file that contains all the planes

Go to File > Open and click Image Stack.
In the Image Stack Open dialog box, select an image file, and click Open.

The Image Scaling dialog box may be displayed; if it is, enter scaling information and click OK to load the image stack

Image order and nomenclature: Single file with multiple images

A multiple-image file such as a PIC or TIF file contains all of the images for one image stack.
The images are interpreted to be sequential images with the first images placed at the top of the stack and subsequent images placed at decreasing Z positions.
The first image is placed at the current Z position.

Open an image stack composed of multiple files

Go to File > Open and click Image Stack.
In the Image Stack Open dialog box, select files and click Open. The Image Opener window opens.

Use the settings and controls in the Image Opener dialog box to specify how you want BrightSLICE software to handle and display the images. Learn more here.
When you have finished reviewing the settings and the order of the files, click the Load button in the Image Opener dialog box to open the files in BrightSLICE software.

If you load an image for which there is no matching lens, BrightSLICE prompts you to create a new lens to match the image scaling. See Creating a lens.

Image order and nomenclature: Multiple single-image files

The order in which multiple images from single-image files are loaded is determined by the order of the files in the dialog box.
We recommend using a naming convention that facilitates image ordering.
If you name a set of images image1, image2, image3, and so on, image10 is placed after image1 but before image2. Instead, number the images as follows: image01, image02...image10, image 11... in order to maintain the correct order.
The images are loaded in the same order as the files appear in the File>Open dialog box.

Viewing image stacks

The top image of a stack is opened at the current Z position of the software. When the stack is loaded, the top image of the stack is displayed.

The status bar at the bottom of the screen provides information about the plane on display.

To navigate through the stack, use the Page Up and Page Down keys on the keyboard.
To view the Z position, use the Z meter or the Image Organizer.
To visualize an entire image stack in a single plane, use Image > Maximum Intensity Projection | Minimum Intensity Projection.

Saving image stacks

Save Image Stack automatically opens following the acquisition of a stack.

To save the modified stack without altering the original file, use File > Save As > Image Stack.
To save a single plane, use File > Save as > Image.

See (Image) Adjustment to learn how adjustments are saved.