Tracking made easy with Volocity 2.

Did you know that with Volocity 2 you can now track moving objects in 3D?

Allow Dr Vipoir to give you a crash course in object classification and tracking.

Before you track you must first classify.

Volocity must be able to identify all the objects that you wish to track in all of the volumes of the time sequence, so it is important that you set up the Classifier correctly before you begin to track.

Remember - the tracking that you get is only as good as the Classifier that you make!

Above is a view from Volocity. The volume that you see is one in a sequence of 10 volumes.

The Classifier will allow us to identify objects on the basis of Intensity, Size and Shape.

There are further tools to;

Reduce noise in selection

Fill holes within objects

Ignore objects that touch the edge of the sample

Separate touching objects.

First, lets make a new Classifier - click on the New Classifier button on the Classifier palette to make one.

This will automatically open the "Edit Classifier" dialog.

For purposes of this demonstration we will use the "Intensity Mode" but just for the record there are 2 other modes namely HSI (Hue, saturation and intensity) and RGB (Red, Green and Blue intensity).

The HSI mode has three histograms that allow the selection of Hue and Saturation as well as Intensity.

The RGB mode also has three histograms that allow the selection of Red, Green and Blue Intensities.

Let’s have a closer look at the histogram.

See those red bars? The Classifier will only include those intensities that fall between the bars. In Volocity you can move the bars to adjust the range, this feature is pretty similar to Density Slicing in Openlab, if you are familiar with that. All pixels intensities below the Lower intensity will be excluded from classification, all pixel intensities above the Upper intensity will be excluded also.

But the Classifier has a whole bunch of extra stuff to make object identification easier.

Firstly there is a size threshold that will allow you to exclude large or small objects from the classification.

Shape recognition will allow you to select objects based on their shape. This tool will match objects to a series of models and exclude those that do not fall within the required parameters.

There is a whole host of shapes to pick from and if none of these seem to fit the bill you can create a custom shape or generate a shape from the current region of interest in the Image view. Remember you can still use the Image view at the same time as the Classification dialog.

If you have selected Custom shape, to edit it use the "Edit" button, see below. This will bring up the "Custom Shape" dialog from which you can modify your shape.

 

 

Moving swiftly on:

The "Fill Holes" option will fill holes in an object (i.e holes that are surrounded on all sides, within the object).

"Reduce Noise" will apply a 3x3x3 median filter to the selection.

"Ignore Objects Touching the Edge of the Sample" will exclude objects that touch the edge of the sample in either X,Y or Z.

"Separate touching objects" will look at the voxel distribution of one object and determine if it is constituted of two or more objects on the basis of the other selection criteria.

At any time when you are using the Classifier, clicking on the "Apply" button will apply the Classifier so that you can take a look at what it has found in the Image view.

If selected, the "Auto Apply" button will do this automatically each time you change one of the Classifier parameters.

When you are happy with the Classifier be sure to give it a name and save it.

Remember you don’t have to use all of the above criteria, think of them as tools to get the best "fit" to the objects that you want to track. Also it is a good idea to try your Classifier out with all of the volumes in the time series before you start, to ensure that it is finding the required objects in each successive volume.

OK, that really was a crash course in the Classifier, now to measure and track.

Go to the "Tools" menu and select "Measure Objects". The "Measure Objects" dialog will appear.

If you want to track you must apply a Classifier and also ensure that you select "Track moving objects".

Clicking on the measure button will give you further options.

These are self explanatory, see the "Track Objects" dialog below. OK, ready to go? Click on the "Track" button.

Once finished a new measurements session will be created complete with all of your tracking measurements, see below.

You can measure; Skeletal length, Volume, Surface Area, Intensity, Centroid, Velocity and Distance.

You can sort any of the measurement columns easily by clicking on the column title. You can also move columns by clicking and dragging to the new position.

I have selected the first five tracks for display. Once you have selected the required tracks go back to the "Image" view to take a look at them.

Plus if you have Volocity Visualization and are able to use the new HR Renderer you can see the tracks in 3D.

And there we have it until next time - Happy Tracking!