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macro:basic_diffusion_analysis
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macro:basic_diffusion_analysis [2019/04/12 13:13] (current) |
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| + | <code> | ||
| + | //Example macro that does a diffusion analysis on a results table of tracking data | ||
| + | //The required format is as generated by the Manual Tracking plugin | ||
| + | //http://rsbweb.nih.gov/ij/plugins/track/track.html | ||
| + | //assuming Results Table column headings; Track > Slice > X > Y | ||
| + | //It requires many tracks and many time points! | ||
| + | //Plots the cumulative mean squared displacement (MSD) per time point | ||
| + | //For a more accurate approach see the time ensemble average example | ||
| + | dis2 = 0; | ||
| + | for (i=0; i<nResults(); i++){ | ||
| + | if (getResult("Slice", i)==1) {setResult("Dis^2", i, 0);} | ||
| + | |||
| + | else{ if (getResult("Track", i)>getResult("Track", i-1)) {setResult("Dis^2", i, 0);} | ||
| + | |||
| + | else { | ||
| + | B9 = getResult("X", i); | ||
| + | B8 = getResult("X", i-1); | ||
| + | C9 = getResult("Y", i); | ||
| + | C8 = getResult("Y", i-1); | ||
| + | disx=(B9-B8)*(B9-B8); | ||
| + | disy=(C9-C8)*(C9-C8); | ||
| + | dis2 = (disx+disy); | ||
| + | setResult("Dis^2", i, dis2); | ||
| + | } | ||
| + | } | ||
| + | } | ||
| + | updateResults; | ||
| + | |||
| + | //get last slice | ||
| + | maxslice = 0; | ||
| + | for (b=0; b<nResults(); b++) { | ||
| + | if (getResult("Slice",b)>maxslice) | ||
| + | { | ||
| + | maxslice = getResult("Slice",b); | ||
| + | } | ||
| + | else{}; | ||
| + | } | ||
| + | |||
| + | //get first slice | ||
| + | minslice = maxslice; | ||
| + | for (c=0; c<nResults(); c++) { | ||
| + | if (getResult("Slice",c)<minslice) | ||
| + | { | ||
| + | minslice = getResult("Slice",c); | ||
| + | } | ||
| + | else{}; | ||
| + | } | ||
| + | |||
| + | //Calculate MSD for each slice and append to a new array (MSD) | ||
| + | MSD = newArray(); | ||
| + | t=0; | ||
| + | time = newArray(); | ||
| + | z = 0; | ||
| + | |||
| + | for (m=minslice; m<maxslice; m++){ | ||
| + | slice = newArray(); | ||
| + | for (l=0; l<nResults(); l++) {if (getResult("Slice", l)==m) { | ||
| + | x = getResult("Dis^2", l); | ||
| + | slice = Array.concat(slice, x); | ||
| + | } | ||
| + | } | ||
| + | t++; | ||
| + | Array.getStatistics(slice, min, max, mean, std); | ||
| + | z = mean+z; | ||
| + | MSD = Array.concat(MSD, z); | ||
| + | time = Array.concat(time, t); | ||
| + | } | ||
| + | //Plot cumulative MSD against time | ||
| + | Fit.doFit("Straight Line", time, MSD); | ||
| + | Fit.plot(); | ||
| + | |||
| + | //Richard Mort 26/01/2013 | ||
| + | </code> | ||
macro/basic_diffusion_analysis.txt ยท Last modified: 2019/04/12 13:13 (external edit)
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