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 physical slide or 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 Main window to place a reference point. If a reference point has not been placed, NeuroInfo 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:
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Open an image before placing a reference point: NeuroInfo will automatically place the reference point in the top left corner of the image.
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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
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.
Joy Track vs. Joy Free
Joy Track is the standard joystick mode. When Joy Track is enabled, the reference point and tracings will remain aligned with the tissue as you navigate with the joystick or field move arrows.
When Joy Free is enabled, the reference point and tracings will no longer remain aligned with the tissue. In other words, the stage will move independent of the tracing data.
If the reference point was not placed accurately resulting in the tissue not being aligned with the tracing data, you can use Joy Free mode to re-align your tissue and tracing data. Once the tracing data is correctly aligned with the tissue, return to Joy Track mode to maintain the alignment.