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Panel Tracking

Eugene Katrukha edited this page Jun 28, 2024 · 4 revisions

If the loaded dataset contains time-lapse data,
an extra "Tracking" panel will appear with under the tracks icon.

TrackingPanel

Curve tracking

To start curve tracking over time, first, a starting "seed" ROI needs to be selected in the list,
and then the train TRAIN button can be pressed.

In the appearing dialog, one can specify the time range/time direction of the tracking and ROI box expansion.
The plugin will interactively search for the ROIs in the next timeframes,
until it can find the next curve or all frames are processed.

tracking_example

Tracking can be stopped by pressing the "train" button again
(during the tracking process its icon changes to "stop" square).

How does the tracking work?

Starting from the initial "seed" ROI (it must be PolyLine3D or LineTrace3D),
the plugin will calculate a bounding box around it.
Then it will move to the next timeframe, find a maximum intensity voxel
in this bounding box and run one-click tracing command on it, generating a new trace.
It will find a bounding box around this new trace ROI, move to the next timeframe, etc.

This is the first implementation of the tracking algorithm,
therefore it is simple and works only with relatively sparse samples.
In the case of dense (many curves next to each other) samples, it can give linking errors.

It is important to realize, that ROIs appearance parameters (line thickness)
will affect the size of the bounding box.
It can be further tweaked by "Expand ROI box search" parameter to increase
(or decrease, given negative values) bounding box in all dimensions by the provided number of voxels.

The bounding box of an ROI can be visualized by double-clicking
on its name in the ROI list (given it is activated in the settings).

Performed one-click tracing will be run with the currently selected parameters,
therefore the settings icon settings button provides a shortcut to change them.

Since curve-like ROIs have a direction, i.e. points are organized from a "start" end
to the "finish" end (marked with a square), the tracking procedure will automatically
align new ROIs. I.e. it will choose "start" and "finish" ends of each new ROI
so that the vector between the ends is most aligned with the vector between ends of the previous ROI.

How the output is organized?

First, a new ROI group is made with the appearance of the "seed" ROI and title of a number.
The "seed" ROI itself is added to it and subsequently all new ROIs.
This is a temporary workaround to organize "curve tracks".
ROIs from different groups can be merged in the Group manager.
When working with "tracks", please, pay attention, multiple ROIs
from the same time point can be present in the same group,
and there are no checks/warnings about it.
The ROIs endpoints alignment procedure (see above) can be applied
to a user-specified group using Align button.

Bounding boxes around traced ROIs or their straightened versions
can be exported to tif files using Extract ROI Box or Straighten commands of Panel Measure.

Extracted tif files will have different sizes, so to join them, UnequalTiffs plugin can be used.

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