ImarisLineage is the new module which builds on the functionality of the powerful and widely used ImarisTrack. ImarisLineage provides tools for accurate automated or manual tracking of dividing cells in 2D/3D time series. ImarisLineage enables creation of an interactive lineage tree where the cell fate can be traced from one progenitor cell to the final generation. The lineage tree can be easily edited (connections between objects and branches, flipping branches) and every selected group of cells (e.g. cells coming from the same progenitor) can be labelled with a different name and color. Additionally, a new range of statistic measures relevant for cell studies are included such as: Cell Cycle Duration, Generation, Time Since First Division, Time Since Previous Division.
In various disciplines including cell biology, embryology and development, stem cell biology or cancer research determining the spatial and temporal origins of progenitor cells is a key factor to understand functions or health/disease state of the tissue or embryo. All those disciplines have benefited greatly from employing techniques such as spinning disk / multi point confocal, (lattice) light sheet, swept field and structured illumination microscopy, which enable long observation of fluorescently labelled living organisms or cell colonies with very limited damage caused by light (phototoxicity). The results of the observations are long 3D time-lapse datasets of multi gigabytes in size with cells dividing, changing their shape and position multiple times.
In ImarisLineage we add on reliable and widely used Imaris 3D particle tracking algorithm to enable automated connecting of tracks of mother and two daughter cells which eventually leads to creation of a lineage tree depicting the genealogical relationships between cells, time between cell divisions and cell generation. In ImarisLineage we provide much improved functionality for manual editing of object detection and connecting objects between timeframes to get the best possible tracking result in complex data sets where automated algorithms might be not optimal. Continuing the software philosophy to give the ultimate user experience, we remain interactivity between raw-dataset, objects and the results of the analysis such as lineage tree (track editor) and statistical parameters which means that objects (or tracks) selected in one mode are highlighted in the other modes enabling corrections, detection of outliers and simplifying analysis. Lineage tracking tool include various presentation modes already available in Imaris like color-coding objects and tracks according to common motility parameters (speed, track length) and is now complemented by the possibility of color labelling cells or groups of cells coming from the same progenitor, cells from the same generation or with the same time between divisions.
Eventually incorporating ImarisLineage tools in the complex 3D/4D image visualization and analysis Imaris platform will broadly expand the analytical possibilities for all researchers analysing the dynamics of the living samples in various disciplines.
The ImarisLineage module includes the full set of algorithms provided with ImarisTrack
integrated into the object “Creation Wizard” of Imaris for “Spots Objects”, “Surface Objects” and “Cell Objects”. All of the tracking algorithmscan be applied to 2D time series or 3D time series (4D) images. Additionally, ImarisLineage includes the ability to automatically detect and track cell divisions. Cell fusions are also automatically detected and tracked. The Lineage algorithm is based on the AutoRegressive Motion algorithm which automatically adjusts to changes from the initial distance constraint (acceleration / deceleration).
The tracking results in ImarisLineage are presented in two windows:
The two views remain interactive as selecting objects, tracks, lineages and branches in the track editor selects the same group of objects in the Surpass view. Also editing one view changes the other.
Track editor in ImarisLineage includes several new visualization and presentation tools such as:
Surpass view in ImarisLineage includes all display and visualization modes known from ImarisTrack and as well as additional visualization tools specific for dividing objects, among them:
The goal of tracking objects is to either measure how they change over time, their motility behaviors, or their cell cycle characteristics. ImarisLineage, in combination with Imaris MeasurementPro, provides a variety of measurements to facilitate analysis.
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.
ImarisLineage offers a set of tools to modify tracks once they have been created. This feature allows manual creation of tracks and lineage trees, editing of the automatically generated lineages, or for the correction of drift in parts of the image that are moving that should not be.
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