/*
* Cell_Adhesion_Assay
* Authors: Pau Carrillo-Barberà
* Department of Cellular & Functional Biology
* University of Valencia (Valencia, Spain)
*/
macro "Cell_Adhesion" {
//choose a macro mode and a directory
#@ String (label=" ", value="High Throughput Analysis
Cell Adhesion Assay", visibility=MESSAGE, persist=false) heading
#@ String(label="Select mode:", choices={"Analysis", "Pre-Analysis (parameter tweaking)"}, style="radioButtonVertical") mode
#@ File(label="Select directory:", style="directory") dir
#@ String (label="Load pre-established
parameter dataset:", choices={"No", "Yes"}, style="radioButtonHorizontal") importPD
#@ String (label=" ", value="![](\"https://live.staticflickr.com/65535/48557333566_d2a51be746_o.png\")
", visibility=MESSAGE, persist=false) logo
#@ String (label=" ", value="Neuromolecular Biology Lab
ERI BIOTECMED, Universitat de València (Valencia, Spain)", visibility=MESSAGE, persist=false) message
//open pre-established parameter dataset
if (importPD=="Yes") {
pdPath=File.openDialog("Select a parameter dataset file");
parametersString=File.openAsString(pdPath);
parameterRows=split(parametersString, "\n");
parameters=newArray(parameterRows.length);
for(i=0; i=qcDebris) {
satPixClass[count]=true;
} else {
satPixClass[count]=false;
}
//quality control: no content
selectImage(counterstain);
run("Duplicate...", "title=QC_nc");
run("8-bit");
run("Subtract Background...", "rolling=50");
run("Enhance Contrast...", "saturated=0.4 normalize");
run("Find Maxima...", "noise=75 output=[Count]");
maxCount[count]=getResult("Count", 0);
run("Clear Results");
if (maxCount[count]>=1000) {
noContClass[count]=true;
} else {
noContClass[count]=false;
}
//quality control & measurements: monolayer
selectImage(counterstain);
run("Duplicate...", "title=QC_monolayer");
totalArea[count]=areaImage;
run("Clear Results");
run("Enhance Contrast...", "saturated="+enhanceCounterstaining+" normalize");
run("Mean...", "radius="+meanCounterstaining);
run("Median...", "radius="+medianCounterstaining);
setAutoThreshold(thresholdMethod+" dark");
run("Convert to Mask");
resetThreshold();
run("Options...", "iterations="+dilateIter+" count=1 do=Dilate");
run("Set Measurements...", "area_fraction display redirect=None decimal=2");
setThreshold(255, 255);
run("Measure");
areaFraction[count]=getResult("%Area", 0);
monolayerArea[count]=totalArea[count]*areaFraction[count];
run("Clear Results");
if (areaFraction[count]=1000) {
trackerCount[count]=0;
}
trackerRatio[count]=trackerCount[count]/(monolayerArea[count]*0.000001);
//close
run("Close All");
selectWindow("Results");
run("Close");
count++;
}
}
}
setBatchMode(false);
//results table
title1 = "Results table";
title2 = "["+title1+"]";
f = title2;
run("Table...", "name="+title2+" width=500 height=500");
print(f, "\\Headings:n\tRow\tColumn\tField\tMean/s.d.\t%SatPix\tDebris\tMaxCount\tNoCont\tTotalArea\tMonolayerArea\t%MonoArea\tQC monolayer\tCells\tCells/mm2");
for (i=0; i