KiT: a MATLAB package for kinetochore tracking

Abstract

Summary: During mitosis, chromosomes are attached to the mitotic spindle via large protein complexes called kinetochores. The motion of kinetochores throughout mitosis is intricate and automated quantitative tracking of their motion has already revealed many surprising facets of their behaviour. Here, we present ‘KiT’ (Kinetochore Tracking)—an easy-to-use, open-source software package for tracking kinetochores from live-cell fluorescent movies. KiT supports 2D, 3D and multi-colour movies, quantification of fluorescence, integrated deconvolution, parallel execution and multiple algorithms for particle localization.Availability and implementation: KiT is free, open-source software implemented in MATLAB and runs on all MATLAB supported platforms. KiT can be downloaded as a package from http://www.mechanochemistry.org/mcainsh/software.php. The source repository is available at https://bitbucket.org/jarmond/kit and under continuing development.Supplementary information: Supplementary data are available at Bioinformatics online.Contact: jonathan.armond@warwick.ac.uk

Complete microtubule–kinetochore occupancy favours the segregation of merotelic attachments

“…To do this we determined the sub-pixel position of GFP-CENPA (centromere/inner KT) and the amino-terminus of Ndc80 (outer KT; using 9G3 antibody) using a MATLAB-based tracking assay (Fig. 2a,b ) 41 , 42 . From the positions of GFP-CENPA and Ndc80 signals in sister-KT pairs we calculated, following correction of Euclidean distances 43 , the intra-KT distance (~103 ± 2.6 nm in control, consistent with earlier studies; 44 N = 4) and the angle between the intra-KT axis and the sister-KT axis (called swivel or k -tilt; Fig.…”

Loss of E-cadherin provides tolerance to centrosome amplification in epithelial cancer cells

“…Here the mask radius r = (2 × dt × v avg ) = (2 × 40 × 0.02) = 1.6 µm, where dt = 40 s is the time lapse, and v avg = 0.02 µm/s is the mean absolute speed of centrosome movement. 3D Gaussians were fitted to the detected spots to find subpixel spot center coordinates, and spots were tracked using KiT spot tracking software ( Armond et al, 2016 ). The manual spot detection module is incorporated into KiT v.1.6.0 (available at https://github.com/cmcb-warwick ).…”

Co-storage and release of insulin-like peptide-5, glucagon-like peptide-1 and peptideYY from murine and human colonic enteroendocrine cells

“…Vesicle detection was performed in all three channels and the positions combined, while removing any duplicates (defined as two coordinates within 2 pixels of one another). A more accurate measurement of vesicle centre position was determined in each channel using mixture-model fitting of 3D Gaussian distributions, resulting in sub-pixel accuracy [17] , [18] . The mean 3D position of all vesicles in each of the three channels were made coincident to remove chromatic aberrations.…”