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Add an animation for branch relative movement
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* Rename spot life cycle to life span of spot
* Replace image to show plugin position of relative movement by plugin path
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@stefanhahmann
stefanhahmann committed Oct 11, 2024
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Expand Up @@ -66,19 +66,19 @@ Mastodon Deep Lineage is an extension of Mastodon. For the full documentation of

### Branch Features

| **Feature name** | **Projections** | **Description** | **Formula/Visualisation** |
|--------------------------------------|----------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------|
| Branch N Leaves | _idem_ | The total number of leaves of a branch spot in the whole track subtree of this branch spot. | ![](doc/features/branch/branchNLeaves.png) |
| Branch N Successors and Predecessors | _idem_ | Total number of successors and predecessors of a branch spot in the whole track subtree of this branch spot. | ![](doc/features/branch/branchNSuccessorsPredecessors.png) |
| Branch Sinuosity | _idem_ | The sinuosity of a spot during its life cycle (cf. [Sinuosity](https://en.wikipedia.org/wiki/Sinuosity)), i.e. how much the track represented by the branch is curved. Values close to 1: almost straight movement. Values significantly higher than 1: winding or meandering movement. Positive infinity (∞), if the spot is at the end at the same position as at the beginning, but has moved in between. | ![](doc/features/branch/branchSinuosityEquation.gif) |
| Branch Average Movement | _idem_ | The average movement per frame of a spot during its life cycle. | ![](doc/features/branch/branchAverageMovementEquation.gif) <br><br> e.g.: <br><br> ![](doc/features/branch/branchAverageMovement.png) |
| Branch Movement Direction | _idem_ | The movement direction of a branch spot represented as a normalized directional vector pointing from the start (spot) position to the end (spot) position of the BranchSpot. | ![](doc/features/branch/branchMovementDirectionEquation.gif) |
| Branch Cell Division Frequency | _idem_ | Number of cell divisions in the subtree rooted at each Branch-spot divided by total duration of branches in this sub-tree | ![](doc/features/branch/branchCellDivisionFrequency.png) |
| Branch Relative Movement* | x, y and z component | The x, y and z components of the average speed of a spot during its life cycle relative to its `n` nearest neighbors. The number of neighbors to be considered can be specified by the users. Default is 5. | ![](doc/features/branch/branchRelativeMovementEquation1.gif) |
| | average speed | The average speed of a spot during its life cycle relative to its `n` nearest neighbors. | ![](doc/features/branch/branchRelativeMovementEquation2.gif) |

'*' The relative movement features cannot be called from the FeatureComputer directly. Instead, they are computed via
the plugin menu: ![](doc/features/relativemovement.png)
| **Feature name** | **Projections** | **Description** | **Formula/Visualisation** |
|--------------------------------------|----------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------|
| Branch N Leaves | _idem_ | The total number of leaves of a branch spot in the whole track subtree of this branch spot. | ![](doc/features/branch/branchNLeaves.png) |
| Branch N Successors and Predecessors | _idem_ | Total number of successors and predecessors of a branch spot in the whole track subtree of this branch spot. | ![](doc/features/branch/branchNSuccessorsPredecessors.png) |
| Branch Sinuosity | _idem_ | The sinuosity of a spot during its life span (cf. [Sinuosity](https://en.wikipedia.org/wiki/Sinuosity)), i.e. how much the track represented by the branch is curved. Values close to 1: almost straight movement. Values significantly higher than 1: winding or meandering movement. Positive infinity (∞), if the spot is at the end at the same position as at the beginning, but has moved in between. | ![](doc/features/branch/branchSinuosityEquation.gif) |
| Branch Average Movement | _idem_ | The average movement per frame of a spot during its life span. | ![](doc/features/branch/branchAverageMovementEquation.gif) <br><br> e.g.: <br><br> ![](doc/features/branch/branchAverageMovement.png) |
| Branch Movement Direction | _idem_ | The movement direction of a branch spot represented as a normalized directional vector pointing from the start (spot) position to the end (spot) position of the BranchSpot. | ![](doc/features/branch/branchMovementDirectionEquation.gif) |
| Branch Cell Division Frequency | _idem_ | Number of cell divisions in the subtree rooted at each Branch-spot divided by total duration of branches in this sub-tree | ![](doc/features/branch/branchCellDivisionFrequency.png) |
| Branch Relative Movement* | x, y and z component | The x, y and z components of the average speed of a spot during its life span relative to its `n` nearest neighbors. The number of neighbors to be considered can be specified by the users. Default is 5. | ![](doc/features/branch/branchRelativeMovementEquation1.gif) |
| | average speed | The average speed of a spot during its life span relative to its `n` nearest neighbors. Example visualization: ![relative_movement_animation.gif](doc/features/relative_movement_animation.gif) | ![](doc/features/branch/branchRelativeMovementEquation2.gif) |

'*' The relative movement features cannot be called from the FeatureComputer directly. Instead, they can be accessed via
the plugin menu: `Plugins > Compute Features > Movement of spots relative to nearest neighbors`

## Hierarchical Clustering of Lineage Trees

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