Automated tracking ofS. pombespindle elongation dynamics

Uzsoy, Ana Sofía M.; Zareiesfandabadi, Parsa; Jennings, Jamie A.; Kemper, A. F.; Elting, Mary Williard

doi:10.1101/2020.10.09.333765

Cited by 3 publications

(4 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Due to the high SNR and straight spindle at a small size (length ≤ 40 pixel), the MCP algorithm does not have the advantages of others. However, in large spindles (length > 40 pixels), the image SNR begins to drop, and the spindle starts to bend, which causes the algorithm [8], [67] trace to fail. Our method starts to show the advantages (Since the proportion of curved spindles in the tested samples is small, MCP does not have an advantage over MtrackJ [66] in distance measurement).…”

Section: Linking Methodsmentioning

confidence: 99%

“…By projecting the microtubule image along the principal axis and fitting the intensity profile curve with a one-dimensional model, they calculate the position of the endpoints by the gradient of the curve. Uzsoy et al [19] developed a method as an ImageJ [20] plug-in specifically for spindle length measurement and tracking. However, those methods do not take the two-dimensional image information into account and can only analyze single straight spindle at a time.…”

Section: Related Work a Spindle Analysismentioning

confidence: 99%

See 1 more Smart Citation

SpindlesTracker: An Automatic Workflow for Spindles Analysis in Time-lapse Images

Li¹,

Jian²,

Hu³

et al. 2022

Preprint

View full text Add to dashboard Cite

Objective: Quantitative analysis of spindle dynamics in mitosis through fluorescence microscopy requires tracking spindles elongation in noisy image sequences. Deterministic methods, which use typical microtubule detection and tracking methods, perform poorly in the case of the sophisticated background of spindles. Methods: In this paper, we present SpindlesTracker, a fully automatic and extensible workflow that can efficiently analyze time-lapse images’ dynamic spindle mechanism. First, we design a novel deep neural network: YOLOX-SP (YOLOX for spindle). It consists of double branches responsible for spindle bounding boxes and endpoints detection. Then an improved SORT algorithm is used to link the same identity in different frames. Subsequently, we pair endpoints that fall into the same spindle bounding box as the spindle poles. Finally, we introduce the minimal cost path (MCP) algorithm to extract the continuous, single-pixel spindle skeleton. Result: SpindlesTracker is evaluated in all aspects of detection, tracking, and skeleton extraction through a fission yeast dataset. It achieves 84.1% mAP in bounding box detection and over 90% accuracy in endpoint detection. And for tracking, the comparison results show that the improved SORT algorithm increases by 1.3% in multiple object tracking accuracy (MOTA) and by 6.5% in multiple object tracking precision (MOTP). In addition, the statistical result shows that the mean error of spindle length is within 1 ?m. Conclude: SpindlesTracker provides a new baseline for multiple spindles analysis. Significance: This workflow could be easily extended to other microtubule or filamentous structures. The code is released on GitHub.

show abstract

Section: Linking Methodsmentioning

confidence: 99%

Section: Related Work a Spindle Analysismentioning

confidence: 99%

SpindlesTracker: An Automatic Workflow for Spindles Analysis in Time-lapse Images

Li¹,

Jian²,

Hu³

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…During anaphase, motor proteins can crosslink and slide apart antiparallel microtubule neighbors, creating extensile force within the spindle and driving spindle elongation 7,9 . In S. pombe, this elongation is quite dramatic, with spindles elongating from hundreds of nanometers in length to roughly 10 μm over the course of mitosis 10,11 . Accompanying spindle elongation, the closed nuclear envelope undergoes a series of shape transitions, from a spheroid, through a peanut-shaped intermediate, to a dumbbell that will ultimately separate into two daughter nuclei (Figure 1A).…”

Section: S Pombe Mitotic Spindles Are Highly Crosslinkedmentioning

confidence: 99%

“…Spinning disk confocal live imaging and laser ablation experiments were performed similar to those described previously 10,13,15 . Live videos were captured using a Nikon Ti-E stand on an Andor Dragonfly spinning disk confocal fluorescence microscope; spinning disk dichroic Chroma ZT405/488/561/640rpc; 488 nm (50 mW) diode laser (240 ms exposures) with Borealis attachment (Andor); emission filter Chroma Chroma ET525/50m; and an Andor iXon3 camera.…”

Section: Live Cell Imaging Laser Ablation and Fluorescence Correlatio...mentioning

confidence: 99%

Mechanical coupling with the nuclear envelope shapes theS. pombemitotic spindle

Begley

Medina

Zareiesfandabadi

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

The fission yeast S. pombe divides via closed mitosis. In short, mitotic spindle elongation and chromosome segregation transpire entirely within the complete nuclear envelope. Both the spindle and nuclear envelope must undergo significant conformation changes and are subject to varying external forces during this process. While the mechanical relationship between the two mitotic structures has been explored previously, much is still left to be discovered. Here, we investigate this relationship by observing the behaviors of spindles and nuclei in live mitotic fission yeasts following laser ablation. First, we characterize these dynamics in molecularly typical S. pombe spindles, finding them to be stabilized by dense crosslinking, before demonstrating that the compressive force acting on the spindle poles is higher in mitotic cells with greater nuclear envelope tension and that spindle compression can be relieved by lessening nuclear envelope tension. We finally examine the differences between the mitotic apparatus in S. pombe and S. japonicus, an evolutionary relative of S. pombe that undergoes semi-open mitosis, and show that S. japonicus mitotic spindles appear to both splay and bend more easily than those of their S. pombe relatives. Altogether, these data suggest that fission yeast spindle crosslinking may be tuned to support spindle extension and oppose nuclear envelope tension.

show abstract

Quantifying yeast microtubules and spindles using the Toolkit for Automated Microtubule Tracking (TAMiT)

Ansari

Gergely

Flynn

et al. 2023

Preprint

View full text Add to dashboard Cite

Fluorescently labeled proteins absorb and emit light, appearing as Gaussian spots in fluorescence imaging. When fluorescent tags are added to cytoskeletal polymers such as microtubules, a line of fluorescence and even non linear structures results. While much progress has been made in techniques for imaging and microscopy, image analysis is less well developed. Current analysis of fluorescent microtubules uses either manual tools, such as kymographs, or automated software. As a result, our ability to quantify microtubule dynamics and organization from light microscopy remains limited. Despite development of automated microtubule analysis tools for in vitro studies, analysis of images from cells often depends heavily on manual analysis. One of the main reasons for this disparity is the low signal-to-noise ratio in cells, where background fluorescence is typically higher than in reconstituted systems. Here, we present the Toolkit for Automated Microtubule Tracking (TAMiT), which automatically detects, optimizes and tracks fluorescent microtubules in living yeast cells with sub-pixel accuracy. Using basic information about microtubule organization, TAMiT detects linear and curved polymers using a geometrical scanning technique. Images are fit via an optimization problem for the microtubule image parameters that is solved using non-linear least squares in Matlab. We benchmark our software using simulated images and show that it reliably detects microtubules, even at low signal-to-noise ratios. Then, we use TAMiT to measure monopolar spindle microtubule bundle number, length, and lifetime in a large dataset that includes several S. pombe mutants that affect microtubule dynamics and bundling. The results from the automated analysis are consistent with previous work, and suggest a direct role for CLASP/Cls1 in bundling spindle microtubules. We also illustrate automated tracking of single curved astral microtubules in S. cerevisiae, with measurement of dynamic instability parameters. The results obtained with our fully-automated software are similar to results using hand-tracked measurements. Therefore, TAMiT can facilitate automated analysis of spindle and microtubule dynamics in yeast cells.

show abstract

Automated tracking ofS. pombespindle elongation dynamics

Cited by 3 publications

References 46 publications

SpindlesTracker: An Automatic Workflow for Spindles Analysis in Time-lapse Images

SpindlesTracker: An Automatic Workflow for Spindles Analysis in Time-lapse Images

Mechanical coupling with the nuclear envelope shapes theS. pombemitotic spindle

Quantifying yeast microtubules and spindles using the Toolkit for Automated Microtubule Tracking (TAMiT)

Contact Info

Product

Resources

About