msd analyzer package  (MathWorks Inc)

Journal: Communications Biology

Article Title: Microtubule polarity determines the lineage of embryonic neural precursor in zebrafish spinal cord

doi: 10.1038/s42003-024-06018-7

Figure Lengend Snippet: a Maximal z-projection of 24hpf zebrafish spinal cord between somites 6–8, showing KIF16Ba (KIF16Ba-mCherry, magenta) and Sara endosomes (GFP-Sara CRISPR Knock in, green) colocalization. b Relative pole B Sara endosomes ratio as a function of spindle-MT enrichment for control (gray, n = 61 NPs) and KIF16Ba MO (green, n = 18 NPs) datasets. Below, GMM clustering of KIF16Ba MO spindle-MT enrichment (DI = 77.8%) with symmetric (blue) and asymmetric (red) clusters. c Sum z-projection of a dividing KIF16Ba MO asymmetric NP (registered t = 75 s) showing Sara endosomes (mCherry-Sara, magenta) and spindle-MTs (GFP-DCX, green). Relative pole B Sara endosomes ratio and spindle-MT enrichment are indicated. Arrows show Sara endosomes symmetric inheritance between the poles (cell contours). a , c Scale bars, 5 μm. d Dynamic of Sara endosomes mean ratio (log scale) as a function of registered time in pole A for control asymmetric (blue; n = 21 NPs) and KIF16Ba MO asymmetric (red; n = 8 NPs) datasets. ANOVA comparison of Sara endosome mean densities as a function of registered time between pole B and pole A ( e ) or cell center and cell sides ( h ) for KIF16Ba MO asymmetric ( e ; n = 8 NPs, 1141 endosomes) and KIF16Ba MO combined datasets ( h ; n = 18 NPs, 1986 endosomes). f Weighted average mean square displacement (MSD) (weighted according to certainty, see methods) as a function of delay for control combined (blue line) and KIF16Ba MO combined (red line) datasets. Blue dashed line, quadratic fit of combined control dataset. Red dashed line, linear fit of KIF16Ba MO combined dataset. R², correlation coefficient (95% confidence). g Average percentage of Sara endosomes in the central spindle area as a function of registered time for the control combined (blue) and KIF16Ba MO combined (red) datasets. Black dashed line indicates departure. d , g , f Shades, relative standard error mean (RSEM).

Article Snippet: Afterward, MSD analyzer package was used with a custom Matlab code to generate \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$MSD(t)=\langle (\varDelta {x}^{2})\rangle +\langle (\varDelta {y}^{2})\rangle$$\end{document} M S D ( t ) = ⟨ ( Δ x 2 ) ⟩ + ⟨ ( Δ y 2 ) ⟩ of each individual track (Fig. ; ).

Techniques: CRISPR, Knock-In, Control, Comparison