Loading and viewing image stacks

Requires a separate license

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

File formats supported

Acquiring image stacks

See Acquiring an image stack

Loading 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 Neurolucida cannot interpret the embedded scaling information, the Image Scaling or Image Scaling and Placement dialog is displayed.

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

Load 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

Load 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 Neurolucida 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 Neurolucida software.

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

Viewing image stacks

The top image of a stack is loaded 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.

Tracing from image stacks

Tracing from image stacks is similar to tracing from a single tissue section.

Neurolucida software keeps track of the Z-depth of your tracing by recording the Page Up and Page Down movements through the sections.

When working with multiple adjacent image stacks, there are two methods:

Trace all visible structures in a given stack before moving to the next adjacent stack. Make sure to connect the endings of the incomplete processes.
- See Tracing trees: endings to learn about ending types.
- See Tracing neurons in serial sections (2D) to learn about tracing through sections.
Follow a given structure through the stacks while tracing.

There is no need for the Serial Section Manager since Neurolucida software treats the different images of the stack like different focal depths of the same section.

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.

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.