TipTracker: automatic tracking of diverse moving objects

Guest post by Arif Ashraf

We study plant roots by observing their developmental stages, physiological conditions and their cell biology. The advent of fluorescent proteins and the power of confocal microscopy have enabled us to track the developmental processes such as cell division, elongation, differentiation, and changes in vital hormone responses. Rapid processes like gravitropism and phototropism are really difficult to follow precisely. In these instances, it is indispensable to track plant roots over time. So far, adapted microscopic techniques have allowed us to mount the samples in a horizontal position. This however can hinder regular root growth and affect gravitropism. Additionally, a plant root is growing continuously, making it difficult to follow its growth over time, as the focus of the microscope needs to be adjusted manually.

Lateral root primordia expressing GFP-plasma membrane marker UBQ10::YFP-PIP1;4 and RFP-nuclear UBQ10::H2B-RFP marker

Figure: Lateral root primordia expressing GFP-plasma membrane marker UBQ10::YFP-PIP1;4 and RFP-nuclear UBQ10::H2B-RFP marker. Published image from TipTracker paper.

From studying the model plant Arabidopsis thaliana, we know that both spatial and temporal data are required to explain any phenomenon in root development. A substantial number of genes that are active during certain developmental stages have specific spatial expression patterns. For example, Cell Cycle Switch 52A 1 (CSS52A1) is expressed exclusively in the transition zone, but is not expressed at all in the meristematic region. Important events require temporal observations over a certain time, for example, gravitropism (minutes), cell division (hours) and differentiation (days).

Jiri Friml and his team tried to solve these problems. They just published (Wangenheim et al., 2017) their new microscopic approach along with a MATLAB® based program, TipTracker, in bioRxiv (and now eLife). This new system will help researchers to follow the vertical growth of root tips through time-lapse imaging, and eventually reconstruct the trajectory of every single root tips and calculate root growth over the time. They used the plasma membrane marker, UBQ10:: YFP-PIP1;4, to confirm the effectiveness of the software, cell plate specific KNOLLE to observe cell division, and the auxin response marker DII Venus to follow gravitropism. Moreover, they tried this approach in non-plant species, such as Zebrafish embryos.

This is an excellent platform to study plant root development extensively. They also have made TipTracker compatible to interact with other various commercial microscopic programmes. The best thing is that the source code is publicly available. So, any lab or any individual may modify and merge it with their system.

Arif Ashraf Arif Ashraf is a PhD student at Iwate University, Japan, and Graduate Student Ambassador of ASPB. His research interest is to understand the hormonal interplay in primary root development of Arabidopsis thaliana. He blogs about plant science at


Von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., & Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife, 6.

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