This repository contains software designed to help quantify the effect on protein localization at specific distances from the edge of a cell before and after a perturbation. This software was originally developed to quantify the effect of CALI perturbation of Cofilin, but the methods should be general enough to work for other proteins and perturbations assuming the caveats listed below are true. Both full cell and kymograph images can be processed. To do this the software follows several steps:
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Identification of the cell edge. This is done using a user provided threshold suitable for identifying the cell body and background regions.
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Binning of Pixel Intensities Back from the Cell Edge. The pixels behind the cell edge are binned according to their distance from the cell edge. The size of the bins are specified by the user.
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Analysis of Binned Pixels. The value of the average, standard deviation and the upper and lower 95% confidence intervals around the mean (T-test based) are calculated for each set of binned pixels. Plots and raw data files are produced.
All of the code is written in matlab and a gui interface is provided. After downloading the software, start MATLAB and change your working directory to the 'src' directory. There are two commands which will start a GUI, one for whole cell and another for kymographs, to gather the needed information concerning your data.
- These methods will not work if your images don't clearly idenfity the cell edge before and after perturbation. Currently, the methods only use the input image set to identify the cell edge. If your protein of interest doesn't mark the cell edge adequately, the distance from the cell edge binning won't work correctly. If there is demand, using a second marker which marks the cell body would be possible.
The software has been used in the following publication:
- EA Vitriol, et al. Instantaneous Inactivation of Cofilin Reveals its Function of F-actin Disassembly in Lamellipodia. Mol Biol Cell, 2013 HTML