Trackosome: a computational toolbox to study the spatiotemporal dynamics of centrosomes, nuclear envelope and cellular membrane
TL;DR: Trackosome is a freely available open-source computational tool to track the centrosomes and reconstruct the nuclear and cellular membranes, based on volumetric live-imaging data, and is a powerful tool to help unravel new elements in the spatiotemporal dynamics of subcellular structures.
read more
Abstract: During the initial stages of mitosis, multiple mechanisms drive centrosome separation and positioning. How they are functionally coordinated to promote centrosome migration to opposite sides of the nucleus remains unclear. Imaging analysis software has been used to quantitatively study centrosome dynamics at this stage. However, available tracking tools are generic and not fine-tuned for the constrains and motion dynamics of centrosome pairs. Such generality limits the tracking performance and may require exhaustive optimization of parameters. Here, we present Trackosome, a freely available open-source computational tool to track the centrosomes and reconstruct the nuclear and cellular membranes, based on volumetric live-imaging data. The toolbox runs in MATLAB and provides a graphical user interface for easy and efficient access to the tracking and analysis algorithms. It outputs key metrics describing the spatiotemporal relations between centrosomes, nucleus and cellular membrane. Trackosome can also be used to measure the dynamic fluctuations of the nuclear envelope. A fine description of these fluctuations is important because they are correlated with the mechanical forces exerted on the nucleus by its adjacent cytoskeletal structures. Unlike previous algorithms based on circular/elliptical approximations of the nucleus, Trackosome measures membrane movement in a model-free condition, making it viable for irregularly shaped nuclei. Using Trackosome, we demonstrate significant correlations between the movements of the two centrosomes, and identify specific modes of oscillation of the nuclear envelope. Overall, Trackosome is a powerful tool to help unravel new elements in the spatiotemporal dynamics of subcellular structures.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Figures
Figure 2. Spatiotemporal relations between cellular structures during early mitosis. (A-F) Example of Trackosome outputs for a representative cell in mitosis. (A) Three dimensional reconstruction of the cellular membrane (green), nuclear envelope (yellow) and centrosomes (red and blue dots). Scale bars: 10 µm. (B) Nuclear membrane and centrosomes at three distinct time stamps. The centrosomes trajectories (red and blue lines) evidence their migration to opposite poles of the nucleus followed by a progressive nuclear deformation. Scale bars: 10 µm. (C) Distance between centrosomes over time. The distance increases gradually during centrosome migration and decreases once the centrosomes start compressing the nucleus. (D) Angles formed between the centrosomes and the nucleus centroid over time. Note how the decrease in the distance between the centrosomes (C) occurs after centrosomes are on opposite sides of the nucleus, corresponding to the highest value for the centrosomes-nucleus angle. (E) Eccentricity of the cellular (green) and nuclear (orange) membranes evidencing that, while the cellular membrane remains morphologically stable, the nuclear membrane undergoes conformational changes after the centrosomes start deforming the nucleus. (F) Angles formed between: centrosomes axis and the 
Figure 4. Nuclear membrane fluctuations vary with the stage of the cell cycle and the physiological treatment. (A) Representative nucleus of each group. The phase of the cell cycle is evidenced by the marked histone (red), taken from the first frame of each video. The nuclear envelope (green) is shown at two different times stamps to illustrate the degree of membrane undulations in each group. Scale bar: 5 µm. (B) Median of the majorant frequency dependent fluctuations, uf, obtained for groups of cells in interphase and early mitosis. The curve for cells fixed with formaldehyde was also included to set the noise limit. (C) Median of the majorant uf obtained for groups of cells in interphase and mitosis, treated with DMSO, nocodazole (NOC) and fixed with formaldehyde. NOC caused a significant decrease of the membrane fluctuations in mitosis. (D) Median across cells of the average FT of the squared fluctuations of each cell, <uf2>, for the groups represented in (C). In logarithmic scales, the <uf2> curves show regions dominated by different frequency dependencies, limited by the solid lines with slopes f0, f-1.5 and f-4. (E) Mean and standard deviation of the log RMS of the fluctuations for all the tested groups. Using a logarithmic scale, the RMS fluctuations distributions are approximately normal and can thus be described by their mean value and standard deviation. 
Figure 1. Evaluation of centrosome tracking. (A) User Interface for centrosome tracking showing the XY, XZ and YZ maximum projections for a video of a mitotic cell with the corresponding automatically identified centrosome positions (red and blue dots). (B) Frame extracted from the three synthetic videos with varying levels of SNR. Centrosomes are inside the red and blue circles. Scale bar: 10 µm. (C) Original trajectory (black) and trajectory obtained by Trackosome (red) for the centrosome on the left in B (red circle), and associated error obtained for both centrosomes. Scale bar: 1 µm. 
Figure 3. Nuclear membrane fluctuations captured with Trackosome. (A-C) The perpendicular membrane displacements measured with Trackosome are sensible to subtle membrane movements. (A) Membrane segmentation (red) of a representative nucleus in prophase (left) and a detailed view of the upper region of the membrane (right) illustrating the difference between defining the fluctuations (black vectors) as perpendicular (top right) or radial (bottom right) movements of the current membrane (red) around the median membrane (black). For the radial displacements, the centroid of the median membrane is used as
Citations
High-Resolution Analysis of Centrosome Behavior During Mitosis.
TL;DR: In this article, the authors describe a method to study mitosis with high resolution, by analyzing the dynamic interplay between centrosomes, nucleus, and cell membrane, using a combination of live-cell imaging and micromanipulation with custom-designed computational tools.
2
A nuclear signal in prophase determines centrosome positioning and ensures efficient mitotic spindle assembly
Joana T. Lima,Jorge G Ferreira +1 more
TL;DR: In this article , the authors investigate how the prophase nucleus contributes to centrosome positioning during the initial stages of mitosis, by using a combination of cell micropatterning, high-resolution live-cell imaging and quantitative 3D cellular reconstruction.
The LINC complex ensures accurate centrosome positioning during prophase
Joana T. Lima,António J. Pereira,Jorge G Ferreira +2 more
TL;DR: The LINC complex is required for accurate centrosome positioning during prophase by mediating dynein loading on the nuclear envelope.
Chromosome condensation mechanically primes the nucleus for mitosis
Vanessa Nunes,Margarida Moura,Débora Vareiro,Nicolas Audugé,Nicolas Borghi,Jorge G. Ferreira +5 more
- 02 Sep 2025
TL;DR: Chromosome condensation generates a mechanical signal that primes the nucleus for mitosis, ensuring timely and accurate transition into mitosis by coordinating cytoplasmic and nuclear events through the LINC complex and SUN proteins, maintaining genome integrity.
References
TrackMate: An open and extensible platform for single-particle tracking.
Jean-Yves Tinevez,Nick Perry,Johannes Schindelin,Genevieve M. Hoopes,Gregory D. Reynolds,Emmanuel Laplantine,Sebastian Y. Bednarek,Spencer L. Shorte,Kevin W. Eliceiri +8 more
TL;DR: TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment and is validated for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells.
3.3K
Steric Interaction of Fluid Membranes in Multilayer Systems
TL;DR: In this article, the steric repulsion energy per unit area of membrane is derived as a function of temperature, membrane curvature elasticity and mean membrane spacing; it is inversely proportional to the square of the latter.
1K
Lamins A and C but not lamin B1 regulate nuclear mechanics
Jan Lammerding,Loren G. Fong,Julie Y. Ji,Karen Reue,Karen Reue,Colin L. Stewart,Stephen G. Young,Richard T. Lee +7 more
TL;DR: It is indicated that lamins A and C are important contributors to the mechanical stiffness of nuclei, whereas lamin B1 contributes to nuclear integrity but not stiffness.
707
Biological imaging software tools
Kevin W. Eliceiri,Michael R. Berthold,Ilya G. Goldberg,Luis Ibanez,B.S. Manjunath,Maryann E. Martone,Robert F. Murphy,Hanchuan Peng,Anne L. Plant,Badrinath Roysam,Nico Stuurman,Jason R. Swedlow,Pavel Tomancak,Anne E. Carpenter +13 more
TL;DR: Each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics are reviewed, focusing on open-source options.
594
Cortical Dynein Controls Microtubule Dynamics to Generate Pulling Forces that Position Microtubule Asters
Liedewij Laan,Nenad Pavin,Nenad Pavin,Julien Husson,Guillaume Romet-Lemonne,Martijn van Duijn,Magdalena Preciado López,Ronald D. Vale,Ronald D. Vale,Frank Jülicher,Samara L. Reck-Peterson,Samara L. Reck-Peterson,Marileen Dogterom,Marileen Dogterom +13 more
TL;DR: It is shown that dynein-mediated pulling forces lead to the reliable centering of microtubule asters in simple confining geometries, and demonstrate the intrinsic ability of cortical microtubules-dynein interactions to regulate micro Tubule dynamics and drive positioning processes in living cells.
445