Image scaling

Overview

When you open an image/image stack and Neurolucida 360 software does not find or cannot interpret image-scaling information, the Image Scaling window will be displayed.

Entering scaling information

There are two main sections in the Image Scaling window: Z–scaling, and X and Y–scaling information for entering scaling information.

Z Scaling Applied to Images

Distance between images: Enter the distance between images (Z-step).

Distance Type: Select Focal or Physical Distance to indicate which category of distance you entered above.

• Focal Distance: Image stacks collected with the program are collected using spacings that describe the focal plane separation.

• Physical Distance: Describes the physical movement of the microscope stage as images are collected.

  If you select Physical Distance, choose the medium for the physical distance between the lens and the specimen and Neurolucida 360 software will autofill the appropriate correction factor. If you select Other, enter the correction factor.

Create sections for this stack checkbox: Check the box to autopopulate the serial section manager with a section for each plane in the image stack, using the Distance between images you specified as the Z-spacing.

X and Y Scaling Applied to Images

X: and Y: µm/voxel: if available, values for the current X and Y scaling will be displayed.

Source of X and Y Scaling: radio buttons

• File: X/Y scaling information comes from the image/image stack file

• Current lens: X/Y scaling information is from the lens currently selected in Neurolucida 360 software. Setting up a lens with X/Y scaling information may save a lot of time if you are working with many images that do not have embedded X/Y scaling information. See instructions for Creating a New Lens.

• User Specified: You can enter the X/Y scaling information manually. Enable this by clicking the checkbox, Override X and Y scaling

Override X and Y scaling checkbox: Click the box, then select the User Specified button (under Source of X and Y Scaling). You can then type in X and Y scaling information.

Applying scaling Information

• Click OK to apply the scaling information to the file you're opening.

  The scaling information will not affect the image/image stack file, but will be saved with your data file (if you choose to save a data file).

• Click Update Image File to save the image/image stack file with the scaling information you entered.

  1. The Update Image File Scaling window will open :

     • Check the box to Allow scaling to be written to the image file, confirming your choice to update the image file.

     • (optional) Check the box to Persist this setting for this session... for files that do not contain scaling information that Neurolucida 360 software can interpret.

     • Click OK.

  2. In the Save As window that opens, navigate to the file storage location and choose a file type from the drop-down menu. We recommend that you save as a .jpx file or use the original file format.

 

Image scaling is not embedded in .tif files generated via slide scanning.

If you load an image for which there is no matching lens, you will be prompted to create a new lens to match the image scaling. See Create a new lens/Edit a lens: Parameters for help.