Reference point overview

Purpose

What is the reference point?

The reference point (or point of origin) has (X,Y,Z) coordinates of (0,0,0) in Cartesian coordinate space and represents the location on the image from which all other points (i.e., all points that constitute traced objects) are calculated.

Each data file contains one reference point. Tracing data are calculated and saved relative to the reference point. If the data file contains multiple sections, the reference point will be located at the top of the first section.

There is only one reference point per file, even if there are multiple sections and slides (or images).

Placing a reference point

Click in the 2D window to place a reference point. If a reference point has not been placed, Neurolucida 360 will automatically place it in the top left corner of an image when it opens.

Many functions are only available after a reference point has been placed.

Where to place a reference point when working with images

A reference point can be, but does not have to be, placed before opening an image:

  • Open an image before placing a reference point: Neurolucida 360 will automatically place the reference point in the top left corner of the image.

  • Open an image after placing a reference point: the location at which the image will open relative to the reference point will depend on which Zoom to fit on load setting is chosen in image preferences.

When a data file is saved, it is automatically linked to the location of the images that were open in the file.  When a data file is opened, the images associated with the data file will automatically be opened in the same location relative to the reference point and tracing data as they were when the data file was saved.

Fiducials

Once a reference point has been placed, it may be useful to place a fiducial. Fiducials are distinctive locations/structures on specimens that you mark as references/landmarks. Fiducials are often used for serial section reconstruction, or to help align a data file with its corresponding experimental sample so that you can resume data collection.

Fiducial points can be marked by placing markers in the 2D window.

Alternatively, you can create a fiducial contour by tracing an accurate contour around a small region that can be easily found again.

See Placing fiducial markers and contours to learn more.