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Panel Tracking
If the loaded dataset contains time-lapse data,
an extra "Tracking" panel will appear with under the
icon.
To start curve tracking over time, first, a starting "seed" ROI needs to be selected in the list,
and then the train
button can be pressed.
In the appearing dialog, you can specify the time range/time direction of the tracking.
The "Search next curve inside" element offers two options:
ROI bounding box and ROI's shape (more constrained).
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 can be stopped by pressing the "train" button again
(during the tracking process its icon changes to "stop" square).
Starting from the initial "seed" ROI (it must be PolyLine3D or LineTrace3D),
the plugin will calculate a bounding box around it or a mask of voxels inside the ROI's shape.
This would be a new "search subvolume".
Then it will move to the next timeframe and find a maximum intensity voxel
in this subvolume and run one-click tracing command on it, generating a new trace.
Then the process is going to be repeated.
The plugin will find a "search subvolume" around this new trace ROI, move to the next timeframe, etc.
This is the first implementation of the tracking algorithm,
therefore it is relatively simple at this point.
The ROI bounding box option works better with relatively sparse samples,
where curves move a lot from frame to frame.
The "ROI's shape" option is better for dense samples with less movement.
It is important to take into account that ROIs appearance parameters (line thickness)
will affect the size of the "next frame search subvolume".
In case of bounding box, its size 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 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.
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.
To color-code ROIs based on time, one can apply LUT using Color 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.
Developed in Cell Biology group of Utrecht University.
Check out Updates history. The plugin and this wiki are under constant development.
E-mail for any questions, feedback, errors or suggestion
or tag @ekatrukha at image.sc forum.