Registering Probe to Head Surface - BUNPC/AtlasViewer GitHub Wiki

If the user has a previous probe design to work from, or a probe has already been designed in SDgui, it can be applied in the AtlasViewer GUI. An SD file can be loaded by clicking “Tools → Import Probe,” and then selecting the desired SD file. The probe will appear as a set of red numbers above the atlas head volume.
Note that if SDgui was launched from within the AtlasViewer GUI, then the SD file information is automatically loaded into AtlasViewer and does not need to be manually imported. In the latter case, the probe is not yet displayed in the AtlasViewer GUI and will not appear until the next step is performed.
Here we use the test.SD file that has been designed in the Designing SD page as an example.

Once a probe design is loaded into AtlasViewer, click “Register Probe to Surface” and wait for the process to complete. This may take a few seconds as it runs through a refinement process that finds a minimum energy configuration for the spring geometries after locking the anchor points in place. More details about the process could be found in this paper https://dx.doi.org/10.1117/1.NPh.2.2.020801. After the process, the probe will be positioned onto the head in a manner that closely approximates the distances specified by the spring connections. Using the rotate/zoom axes buttons allows the atlas head to be rotated and magnified to facilitate viewing the resulting probe registration.



By unchecking “Hide Probes”, “Hide Springs” and “Hide Dummy Optodes” in the Probe box, while “Hide Meas List” remains checked, it becomes apparent how AtlasViewer positions the optodes on the surface of the head using spring interactions, as shown in the following figure.




In this view, the color of the spring designates the deviation of the spring length in millimeters from the target separation of the two optodes as defined in the SD file. The thresholds for setting the colors are given by the two numbers in the edit box just to the right of the “Hide springs” box. The default values are 3 and 10 mm.
The user can set these values by editing the numbers in the edit box when “Hide Springs” is unchecked.

• If the absolute value of the deviation is less than the first number (i.e. 3 mm) then the spring is black.
• If the absolute value of the deviation is between the first and second numbers then the spring is cyan or yellow for a negative or positive deviation, respectively.
• If the absolute value is greater than the second number (i.e. 10 mm) then the spring is blue or red for a negative or positive deviation, respectively.

The interoptode springs in this example should all be black, while the optode-to-dummy optode springs will be red, which is to be expected since their lengths were set to −1, designating them as weaker and thus only used for orientation purposes. If the user desires to have different ranges of accuracy displayed, they can easily edit the thresholds in the edit box.