ImarisTrack

Discover the Meaning of Motion

 

ImarisTrack is the most powerful commercially available live cell imaging, tracking  & analysis software that rises to the challenge of monitoring temporal changes in biological systems (2D and 3D images over time). ImarisTrack is based on a choice of multiple sophisticated manual and automatic tracking algorithms and also includes an intuitive and interactive track editing tool if manual correction is necessary. Together this set of tools offers researchers the confidence and support necessary for analysing extremely large and complex data sets. ImarisTrack also provides translational and rotational drift correction which allows researchers to unravel key individual biological events which take place within a complex and dynamic environment (e.g. track a group of defined cells within a developing embryo).

Overview


A major challenge to any tracking software is the fact that segmented objects at different time points have no relationship between the time points. The job of a good tracking software package is (i) to correctly identify the objects that should be all part of the same track, (ii) to accurately join them as part of a track, and (iii) to precisely track the objects position even if on occasion the object may disappear or reappear. Tracking software should also deal with objects that remain stationary and happen to be in the path of another mobile object. This may lead to artefacts and inaccuracies in the tracking process that can be easily spotted and corrected manually.    

ImarisTrack allows selection from a variety of manual and automatic tracking methods to join these independent objects into tracks easily. Sophisticated algorithms in ImarisTrack can handle objects that appear or disappear. It can use previous object speed and directionality for predicting future positions as well as weighted intensity information to enable the most accurate tracking possible even for complex, densely populated, dynamic and noisy images. In addition to these automated tracking options, ImarisTrack offers an intuitive (click-drag-drop) and flexible track correction tool to allow users to manually edit  individual tracks once the automatic tracking is finished. The track editing window shows an illustration of each object on the screen and its connection (track) to objects at other time points.  Changes or selections made in the editing window immediately appear in the image view in 3D space providing real-time interactive editing.

In combination with Imaris MeasurementPro, ImarisTrack provides statistical data that is specific to tracking such as straightness and length of tracks; speed, variability and duration tracks; displacement of movement of the object and many more. Because ImarisTrack links independent objects together in a track, users can look at changes in all previously calculated statistical parameters. You can measure distances in 3D and 4D, areas, volumes, voxel intensities, objects’ tracks as well as identify objects based on intensity, size and their changes over time for each set of objects. Like for any other statistical parameter calculated with Imaris MeasurementPro, tracks can be sorted, filtered, classified, selected and grouped with the exact same interface described for Imaris MeasurementPro, but based on these track specific statistics. Likewise, track statistics can be exported to external programs for analysis.

Additionally, ImarisTrack provides a variety of methods to display the tracked results with the original data. This allows for easy verification of the tracking results and the possibility to present the data in a manner that outside observers can quickly understand.

Features


ImarisTrack functionality requires Imaris. For statistical output, ImarisTrack functionality requires Imaris MeasurementPro.

(1) Track Construction – Algorithms

Integrated into the object “Creation Wizard” of Imaris for both “Spot Objects” and “Surface Objects”, ImarisTrack provides an advanced set of algorithms to manually or automatically group segmented objects into tracks over time. All of the tracking methods can be applied to 2D time series or 3D time series (4D) images.

  • Brownian Motion Model - Simple to use Brownian model finds the most likely path connection in any direction, within a distance constraint.
  • Autoregressive Motion Model - Straightforward Auto-regressive mode can automatically deal with changes from the initial distance constraint (acceleration / deceleration), and improves tracking accuracy for objects with strong directionality.
  • Autoregressive Motion Expert - Auto-regressive “expert” tracking provides you with full control of the algorithm, for challenging tracking problems not solved by the easy modes. Adjust for intensity similarity among candidates for track connections.
  • Gap Close – Applicable to Brownian or Autoregressive motion models this option allows you to specify the number of frames for which the algorithm continues to search for candidate objects after the object disappears. This feature is needed for objects that either turn on and off by design or that move in and out of focus.
  • Fill gap with all detected objects - use this option to perform prediction of the objects' expected positions for particular time point. Their tracks can be then generated by connecting objects over time and by taking into account objects' expected positions in places where their signal was not detected. Fill gap works on Spot, Surface and Cell objects.
  • Connected Components – “Connected Components” is often the best choice for high quality images with frequent time sampling, and is also used for automatic detection of objects that divide or fuse.
  • Manual tracking – this option can be used either when automatic tracking algorithms require modifications, or can be used to create an entire track from scratch.



(2) Visualization

Inspecting or presenting a tracking result visualized as a line connecting all the positions of an object is a natural starting point, but more innovative and flexible options are needed to make sense of images as the X, Y, Z, and t dimensions increase in size, or as the density of objects in the image increases. ImarisTrack not only provides the right variety of tools to clarify complex positional data, but also can map object size, time index, and other statistical information directly to the tracks.

  • Track Display – Directly visualize the track as an exact path of the object, using a line for high contrast, or a shaded cylinder for enhancing relative depth perception. View the objects on the tracks, the center point of the object on the track, or just the track alone when the objects might obscure or complicate the view.
  • Displacement - The displacement arrow highlights the shortest path between the start and the end points for any given track. ImarisTrack can use a shaded 3D arrow to improve the viewer’s perception of overall direction and displacement in 3D space.
  • “Dragon Tail” – Customize the length of the track path for visual clarity by displaying the path as a dragon-tail, which only shows the selected number of time points. “Dragon Tail” visualization of the track is a perfect example of the quality innovations that come from the established skill and experience in multidimensional microscopy of Biplane’s programmers. With this method, you can interpret hundreds of tracks within a small space without cluttering the view, as can easily happen with more traditional track viewing approaches.
  • Color Coded Tracks – Tracks can be color-coded according to any specific statistical values (in combination with Imaris MeasurementPro) or may be color-coded based on time.
  • Versatility - As long-time users of Imaris know, the greatest power of Bitplane software often comes from the ability to simultaneously use more than one approach in a single visualization or analysis. For a single figure or movie, show some tracks in blue, some in red; some as lines, some as cylinders, view the displacement and volume change of some tracks, and show Dragon Tail paths for others. With ImarisTrack, it’s no problem!



(3) Measurements

The main point of tracking objects is almost always to measure how they change over time, ImarisTrack, in combination with Imaris MeasurementPro, provides a variety of measurements to facilitate analysis.

  • Track Specific Statistical Values – Duration, length, straightness, displacement X, Y, Z and total, squared displacement, velocity X, Y, and Z, average speed, instantaneous speed, speed variability, quality of fit to autoregressive model (short-term predictability) - per-axis or mean of all axes.
  • Object Time Dependant Statistic Values – Changes in size, shape and intensity over time.  In addition to being displayed in a table, these statistics are shown as a graph.  You can select a time point of interest in the graph and the visual view in surpass changes accordingly.
  • Filtering, Sorting, Classifying and Grouping – Using interface described for Imaris MeasurementPro, tracks may be filtered sorted, classified and grouped based on the track specific parameters.
  • Selection – In addition to selection based on any of the filtering, sorting and classification methods, tracks may be selected by clicking on the track in the visual view or by clicking a segmented object that is associated with a track and choosing a track specific statistic.
  • Export – Track statistics can be exported as .csv, Excel .xml or native Excel .xls files. The statistics can be exported for one track, a group of tracks, or all tracks. Additionally, statistics can be exported for one, a selection or all measured parameters. Finally, it is possible to specifically export the data needed to replicate any of the interactive plots Imaris creates/shows. The statistics of all segmented objects associated with a track can also be exported.



(4) Editing

ImarisTrack offers a set of tools to modify tracks once they have been created. This feature allows manual creation of tracks, or editing of automatically generated tracks, or for the correction of drift in parts of the image that are moving that should not be.

  • Translational and Rotational Drift Correction – ImarisTrack can track all objects in an image, even objects that should be stationary. Once tracked an object or series of objects that should not be moving can be selected. Then positions of all other objects within the image are corrected based on this anchored object or average of the selected objects. This positional shift results in drift correction in the image and the anchor object(s) expected to be stationary will be stationary in the resulting image.   The drift correction allows the detection of the true movement of the other objects of interest. In addition to translational drift correction, rotational drift correction can be utilized if at least three objects in various parts of the 3D image, that should not be moving, are selected as a basis for drift correction.
  • Track Editing – Sometimes automatic tracking is not perfect and researchers need a system to correct for errors.  ImarisTrack makes track editing quick and easy. If an object does not belong in a track after automatic tracking, simply select that object in the visual view and correct the track in the Track Editor panel. It is possible to disconnect, reconnect, and modify the track connections for all tracks. If your image contains many tracks and only a few of them need correcting, you can select only those tracks that have to be inspected manually without the need of going through thousands of correctly assigned tracks.
  • Single Spot Object Tracking – With ImarisTrack, researchers can track single spot objects in the image rather than all the objects in the image.  This is a benefit for researchers that only are interested in specific objects within an image as it saves on computation time and makes display simple.  Single object tracking can be utilized immediately by cancelling out of the automatic creation wizard and going to the edit tab or can be utilized once automatic creation has completed.

Datasheet


General

  • Tracks can be created from Surfaces or Spots objects
  • Tracking can be selected in the first step of creation wizard for Surfaces and Spots if the ImarisTrack license is active
  • Tracking can be performed on 2D+time or 3D+time images
  • Tracks establish a time dependant relationship between objects

- All segmented objects (Spots or Surfaces) initially have no relationship to one another between time points
- Tracking links the objects, thus identifying one object as really being the same object at subsequent time points
- Tracks allow the quantification of movements of objects and changes in size, shape, and intensity

 

Visualization

  • Track Path Display

- Display as a line or a cylinder
- Change the diameter of the cylinder or line
- Turn on or off as needed
- Color code the line or cylinder based on time, a single base color, or on any calculated statistics (Requires Imaris MeasurementPro)
- Display the line as a “dragon tail”- the connections for the last X number of time points rather than all time points

  • Displacement

- An arrow showing the distance and direction between the first and last point of the track
- Turn on or off as needed
- Color and change diameter as desired

  • Object Display – As described for Imaris, Spot and Surface objects can be displayed along with the track as a center point representation, the actual segmented object, a scaled down version of the actual segmented object, or can be hidden to show only the original data and the track

 

Statistics (Requires both Imaris MeasurementPro and ImarisTrack)

  • Track Specific

- Duration, length, straightness
- Displacement,  X, Y, Z, total displacement, squared displacement
- Instantaneous velocity X, Y, Z, velocity, average speed, instantaneous speed, speed variability
- Quality of fit to autoregressive model- per-axis or mean of all axes

  • Object Specific – Spots or Surfaces

- Changes in size, shape and intensity over time.
- All statistics as described for objects in the MeasurementPro module become linked on a per track basis
- A plot of each object's statistics per time point is created when the object is selected. Selection in the graph changes the visualization time point.

  • Export

- Export for one track, a group of tracks or all tracks
- Exports both track specific and object specific statistics for each track
- Export one, a selection or all calculated parameters

  • Annotation

In combination with Imaris InPress, once objects of interest have been selected the image  can be annotated with any calculated  statistical parameter in 3D space.  The resulting annotations can be exported as a figure with Imaris InPress.

 

Algorithms

  • Tracking algorithms are used for the creation of tracks for surface or spot objects

  • Brownian motion algorithm

- Finds the most likely path connection in any direction, within a distance constraint.

  • Autoregressive motion algorithm

- Utilizes direction and speed information from previous motion of the object to predict future locations to search of an object
- Searchers within a distance constraint around the predicted location
- Excellent of objects that have directed movement

  • Autoregressive motion expert algorithm

- Utilizes all the parameters of the autoregressive motion algorithm
- Adds the possibility to use object intensity as a criteria for tracking
- Excellent for when objects of varying intensity cross

  • Connected components algorithm

- Connects objects that would physically overlap if adjacent time points where superimposed on each other
- Good only for extremely high time resolution
- Allows for merge and split of objects

  • Manual tracking

- It allows the user to track spot or surface objects within a time-resolved data set by manually specifying the object location in each time point. This mode can be applied when automatic algorithms need user input and/or modifications.
- Auto-connect to selected spot box option activates manual tracking and advances to next time point when a new object is added or an existing is selected

 

  • MaxDistance

- The maximum distance that an object moves between two adjacent time points
- Utilized in the Brownian motion and autoregressive algorithms as the distance constraint

  • MaxGapSize

- The maximum number of time points that the algorithm searches for an object that disappears
- Utilized in the Brownian motion and autoregressive algorithms
- Prevents two separate tracks being created for one object
- Excellent for object that appear / disappear or turn on /off
  • Fill gaps with detected objects

- This option will try to fill gaps in the track caused by a temporary disappearance of the tracked object.  Fill gaps will assume the object's expected positions for given time point. The track is subsequently generated by connecting objects over time and by taking into account objects' expected positions in places where their signal was not detected. Fill gap works on Spot, Surface and Cell objects.



Editing

  • Uses the Autodepth algorithm for easy selection of tracks or objects in 3D space for editing

  • Fix misconnected/disconnected tracks in the intuitive Track Editor panel.

- Allows for manual correction of problematic areas and connections within tracks
- Point and click method is easy to use
- Click-drag-drop to create new connections
- Allows for objects that split and merge

  • Correct object’s translational and rotational drift

- After the objects are tracked you can select an object (or group of objects) that should not be moving during your time series and use it (them) as an anchor/reference point(s).
- Images are shifted on a frame to frame basis so that the selected anchor objects no longer move and the true movement of the other objects can properly be assessed.

  • Rebuild – The tracking algorithm may be repeated without the need for recreating / re-segmenting the objects

 

Filtering

  • Like surfaces and spots objects, tracks may be filtered as part of the creation wizard based on any of the statistical parameters calculated for those tracks.

  • Tracks may also be filtered within the filter tab after creation is complete.

Videos


Edit Tracks

Watch this video tutorial and learn how to interact with tracks if tracking needs to be adjusted.

Watch Imaris Edit Tracks Tutorial movie (5:54) Download Imaris Edit Tracks Movie

3D Tracking

Watch this video to learn how to identify, follow 3D-objects over time, display their paths and analyze their movements.

Watch Imaris 3D Tracking Tutorial movie (11:33) Download Imaris 3D Tracking Movie

2D Tracking

Watch this video to learn how to identify, follow 2D-objects over time, display their paths and analyze their movements.

Watch Imaris 2D Tracking Tutorial movie  (11:33)  Download Imaris 2D Tracking movie

Surface Rendering Surface and Spot Objects Keyframe Animation Volume Rendering Spot Objects Region of Interest Surface Scissors Volume Rendering Volume Rendering
Show Cases

4D Particle Tracking
Dr. Willy Supatto and colleagues, California Institute of Technology, USA
Living systems rely on fluid dynamics from embryonic development to adulthood. One well known example is the specification of the left-right axis in vertebrates, where beating cilia generate a directional flow >>>

4D-Tracking with Imaris
Dr. T. Worbs, Prof. R. Förster and, Hannover Medical School, Germany
Automated tracking of T-lymphocyte migration: The present study demonstrates that chemokine receptor CCR7 signaling enhances the motility of CD4+ T cells. >>>


References
  • Schober H et al, Genome Res., Feb 2008; Controlled exchange of chromosomal arms reveals principles driving telomere interactions in yeast >>>
  • Lämmermann T et al, Nature, May 2008; Rapid leukocyte migration by integrin-independent flowing and squeezing >>>