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AxonTracker 3D Manual

I. Loading the data

In order to load the data, click

on the “Load Data” option from

the “Data” menu. Alternatively,

data can also be loaded using

the “New” shortcut in the main

window. Once the data is

loaded, it is rendered in the

main window along with a

binding box, coordinates and

labeled axes for reference. The

intensity of the rendered data

can be changed with a vertical

slider bar provided next to the

rendering area to the far right.

Moving the slider up or down

will change the brightness of

the rendered data.

II. Tracking the centerlines

To begin tracking the axon centerlines, an object must first be added to the list of objects

(Alternatively, an object can be

deleted by clicking “Delete Object”

button). For each object created, an

initial point must be entered to

begin tracking. This can be done by

clicking on the “Edit centers”

button. This will open a 2D view of

the dataset at three orthogonal

directions. The locations of these

2D images can be adjusted by the

respective sliders under each of

these images. By enabling the “Add

Point” button in this window, a

center point in one of the three

images can be chosen. Once a point

is chosen, the remaining two windows automatically adjust their position to show this center.

The chosen seed is displayed as a red dot. “Delete Point” button can be used to remove the

point that has been added.

A “Play/Pause” button has been provided in both the main window and the orthogonal view

window for convenience. This button starts the tracking of the object selected in the main

window (the centerline being edited in the orthogonal view window). Please note that there is

a small delay before the actual tracking begins (usually about 3-4 minutes), as the software

estimates the most probable locations of the centers. This is done only once for each dataset

and there is no delay for subsequent objects being tracked. The data can be preprocessed to

remove any noise present, before starting the tracking. This can be done by “Data->Pre

Processing” menu.

As the objects are tracked, the (3D) centerlines are shown in the render window in real time. If

the orthogonal views are open, the new center is shown as a red dot in window. If any

previously tracked centers are present in the current view (2D), they are shown by green dots.

III. Editing the centerlines

In case of a failure to find the next center point due to low contrast and/or intensity, a

notification will pop up asking to add more points to the current centerline. In such a case, add

at least 2-3 points on the axon to guide the centerline. When done adding the centers, click on

the play/pause button to resume tracking.

If during tracking, the centerline “jumps” from one axon to another due to poor contrast at the

boundaries, the

tracking can be

paused and the

wrong centers

can be deleted

and corrected

using “Delete

Point” button

and “Add Point”

button. This can

be observed by

having the


views (2D) open

during tracking, or by clicking “Show Tracking History” button at any time during the tracking

(Disabled while “play/pause” button is active).

Note: While adding new points, add them close to the last center tracked by the algorithm.

Spacing the points too much causes errors in tracking.

Note: Adding new points in the opposite direction of tracking will cause erroneous results.

IV. Visualizing the tracking results

The tracking results can be visualized by clicking on the “Objects” tab. The objects that have

been tracked so far will be listed along with a check-box on their left hand side. To visualize an

object from the list, check the object and click the “Update Scene”. “Check all” and “Uncheck

All” buttons have been provided for convenience. The 3D rendering window will be updated

according to the selection. A “Snapshot” button has been provided just above the render

window to save the 3D rendering, along with any centerlines added to the scene, in a “.png”


Alternatively, the tracked

objects can be visualized in 2D

as well. To do this, click on the

radio button next to one of the

MIP (Maximum Intensity

Projection) views. This opens

up a 2D MIP image along with

similar controls for 3D case. To

visualize an object, check the

object from the list, and click

“Update Scene”. The

“Snapshot” button serves the

same function as in the 3D


V. Saving your work

To save the tracked centerlines to disk, click on the “Save Centerlines” button, which is present

in the “Tracking” tab. Alternatively, this can be done by clicking on the shortcut “Save Tracking”

or by “Centerlines->Save Centerlines”. The tracking can be paused at any time and saved to disk

in this manner. Loading the saved centerlines can be done in a similar fashion with “Load

centerline” button, “Open saved centerlines” shortcut, or “Centerlines->Load Centerlines”.

Please note that after loading centerlines, all the current centerlines in the list will be erased.

The centerlines can be saved in two formats, Binary and Comma Separated Value (CSV) format

(can be read by Microsoft Excel). The former can be used for saving and loading the centerlines,

whereas the latter can just be used for saving the centers.

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