Differences
This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
usage:tracking [2020/01/22 17:31] – [Outputs] pseudomoaner | usage:tracking [2021/03/06 15:44] (current) – pseudomoaner | ||
---|---|---|---|
Line 20: | Line 20: | ||
Some features can also be useful for telling the algorithm when something has gone wrong. For example, an object may mis-segment, | Some features can also be useful for telling the algorithm when something has gone wrong. For example, an object may mis-segment, | ||
- | |||
- | Pairs of features that are correlated should be avoided. For example, for rod-shaped cells, cell length and cell area are approximately proportional to one another. Due to this statistical redundancy, the linking metric used by the tracking algorithm will weight changes in cell length approximately twice as strongly as it should do. In this case, a selection of only one of the two features should be made. | ||
The checkboxes in the **Features for inclusion** panel allow you to choose the features within your dataset that fulfil the above criteria. | The checkboxes in the **Features for inclusion** panel allow you to choose the features within your dataset that fulfil the above criteria. | ||
Line 37: | Line 35: | ||
Once you have chosen the features you wish to include, click **Calculate!**. Once this has finished processing, a histogram will appear in the top-left hand axes. This can be used to select the first of the user-defined parameters, denoted as **Proportion of low-quality links to use in training**. Changing the value of this parameter with either the slider or the edit box will alter the position of the vertical red line plotted on top of the histogram. | Once you have chosen the features you wish to include, click **Calculate!**. Once this has finished processing, a histogram will appear in the top-left hand axes. This can be used to select the first of the user-defined parameters, denoted as **Proportion of low-quality links to use in training**. Changing the value of this parameter with either the slider or the edit box will alter the position of the vertical red line plotted on top of the histogram. | ||
- | This histogram indicates the initial distribution of frame-frame link distances, before any feature reweighting has been performed. Typically, it contains two peaks, one towards the left containing accurate links, and one further to the right containing the inaccurate links. If this is the case, it is usually best to select the **Proportion of low-quality | + | This histogram indicates the initial distribution of frame-frame link distances, before any feature reweighting has been performed. Typically, it contains two peaks, one towards the left containing accurate links, and one further to the right containing the inaccurate links. If this is the case, it is usually best to select the **Proportion of training |
{{ : | {{ : | ||
Line 43: | Line 41: | ||
If there are more than two peaks, choose a value that splits the left-most peak from the others. | If there are more than two peaks, choose a value that splits the left-most peak from the others. | ||
- | If you see only a single peak, try changing the **Features to use for model training** radio button selection to **All features**. This will switch the training portion of the algorithm from using only object position | + | If you see only a single peak, try changing the **Features to use for model training** radio button selection to **All features**. This will switch the training portion of the algorithm from using only object position to assign the initial set of links to using the entire set of selected |
Once you have finalised your selection, click **Calculate!** again to generate your final statistical model of the dataset. | Once you have finalised your selection, click **Calculate!** again to generate your final statistical model of the dataset. | ||
Line 70: | Line 68: | ||
* Green and blue objects have been assigned links between the two frames. The colour of linked objects remains constant between the two frames. | * Green and blue objects have been assigned links between the two frames. The colour of linked objects remains constant between the two frames. | ||
* Yellow objects are objects in frame A that have not had a link assigned to an object in frame B, as their associated score was below the currently selected linking threshold. | * Yellow objects are objects in frame A that have not had a link assigned to an object in frame B, as their associated score was below the currently selected linking threshold. | ||
- | * Purple objects are objects in frame B that have not had a link assigned | + | * Purple objects are objects in frame B that have not had a link assigned |
In the case above, most objects have been assigned links and are correspondingly coloured green or blue. The exception to this is the pair of objects in the bottom left-hand corner of the image. They are initially segmented correctly in frame A, but become fused in frame B. Because of this mis-segmentation, | In the case above, most objects have been assigned links and are correspondingly coloured green or blue. The exception to this is the pair of objects in the bottom left-hand corner of the image. They are initially segmented correctly in frame A, but become fused in frame B. Because of this mis-segmentation, | ||
Line 90: | Line 88: | ||
Firstly, it can be used to verify that each feature is properly normalised. If they have been properly normalised, the displayed scatterplot should be isotropic (radially symmetric) and centred on the origin. Below are examples of well-normalised (left) and poorly normalised (right) features: | Firstly, it can be used to verify that each feature is properly normalised. If they have been properly normalised, the displayed scatterplot should be isotropic (radially symmetric) and centred on the origin. Below are examples of well-normalised (left) and poorly normalised (right) features: | ||
- | {{: | + | <WRAP half column centeralign> |
- | {{ : | + | {{ : |
+ | </ | ||
+ | |||
+ | <WRAP half column centeralign> | ||
+ | {{ : | ||
+ | </ | ||
In the second case, the ' | In the second case, the ' | ||
Line 124: | Line 127: | ||
=== Track length filtering === | === Track length filtering === | ||
- | Various processes can generate short tracks that are not useful for analysis. Mis-segmentations can result in ' | + | Various processes can generate short tracks that are not useful for analysis. Mis-segmentations can result in ' |
{{ : | {{ : | ||
Line 146: | Line 149: | ||
<code matlab> | <code matlab> | ||
- | | + | |
- | | + | |
- | <\code> | + | </code> |
- | + | ||
+ | for all a, b, c and d. These expressions generalise for all other fields than trackableData.Centroid and procTracks.x. | ||
* **procTracks: | * **procTracks: | ||
* **linkStats: | * **linkStats: | ||
Line 167: | Line 172: | ||
* **x** and **y:** The instantaneous coordinates of the object over time. Each is a $t \times 1$ vector. | * **x** and **y:** The instantaneous coordinates of the object over time. Each is a $t \times 1$ vector. | ||
- | * **smoothx** and **smoothy: | ||
* **theta** and **vmag:** The instantaneous direction of motion (in degrees) and speed of the object. Each is a $(t-1) \times 1$ vector. | * **theta** and **vmag:** The instantaneous direction of motion (in degrees) and speed of the object. Each is a $(t-1) \times 1$ vector. | ||
- | * **smoothTheta** and **smoothVmag: | ||
* **times:** The timepoints the object' | * **times:** The timepoints the object' | ||
* **length:** Total length (in timepoints) of the track. | * **length:** Total length (in timepoints) of the track. | ||
* **start** and **end:** Start and end timepoints of the track. | * **start** and **end:** Start and end timepoints of the track. | ||
* **age:** The age of the object relative to the start of the track at each timepoint. Equivalent to **times** - **start**. | * **age:** The age of the object relative to the start of the track at each timepoint. Equivalent to **times** - **start**. | ||
+ | * **interpolated: | ||
Depending on the options selected in the [[usage: | Depending on the options selected in the [[usage: | ||
Line 187: | Line 191: | ||
===== Video demonstration ===== | ===== Video demonstration ===== | ||
- | {{ youtube>rSnvglvt-rE?large }} | + | ====Part 1==== |
+ | {{ youtube>EW4hl439Xp4? | ||
+ | |||
+ | ====Part 2==== | ||
+ | {{ youtube> | ||