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sakulab-software/BQuant
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BQuant v0.1 Wong JH et al. Basic proline-rich protein-mediated microtubules are essential for lobe growth and flattened cell geometry. Plant Physiol, 2019, https://doi.org/10.1104/pp.19.00811 ----------------------------------------------------- # Data format - Prepare a csv file in which the fluorescence intensity series is entered vertically. - If you want to analyze more than one series, arrange the vertical series horizontally. Example: ( Linescaned intensity index ---->) 1141.1, 219, 375.4 949.69, 263.86, 369.16 879.32, 171.33, 512.53 629.82, 118.64, 877.86 506.09, 236.84, 1417.47 305.48, 473.64, 1944.38 240.93, NaN, 1739.57 316.47, NaN, 1541.18 298.35, NaN, NaN 289.82, NaN, NaN - To match the longest series, enter "NaN" where there is no number in the short series. - Place data files in the "data" folder. ----------------------------------------------------- # Analysis procedure - Basically you just edit and run the MATLAB script "main.m". - Edit "file", "dx", and "pp". "smooth_level" is optional. - The analysis result of each step is saved in the "data_working" folder. 0. step0_backgrund_subtraction.m - Remove gradient spots in microscopic images. - Save images and feature values. 1. step1_estimate_MT_location.m - Smooth intensity data by gaussian filter to reduce small noise - Estimate MT locations as: *positive peaks *Inflection points - Save images and feature values. 2. step2_gaussian_fitting.m - Fit Gaussians to intensity series by optimization algorithm without using any library for calculation. - Determine the parameter that maximizes the posterior distribution by locally minimizing the likelihood with the Gaussian location as the prior distribution. - Save images and feature values. NOTE: Calculation time will be required depending on data size. 3. step3_quantification.m - Compute statistics on height, width, and area of Gaussians. - Draw histogram and Gamma distribution fitted to the data. - Save the values in csv format in the 'data_stat' folder.
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