/*
* 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)"}, persist=true, style="radioButtonVertical") mode
#@ File(label="Select directory:", persist=true, style="directory") dir
#@ String (label="Load pre-established
parameter dataset:", choices={"No", "Yes"}, persist=true, style="radioButtonHorizontal") importPD
#@ String (label="Save ROIs:", choices={"No", "Yes"}, value="Yes", persist=true, style="radioButtonHorizontal") saveROIs
#@ 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", prominence, 0, 2, "pixels");
Dialog.addSlider("Threshold", 0.01, 1.00, thresholdTracker);
Dialog.addNumber("Min object size", minSize, 0, 2, "pixels");
Dialog.setInsets(0, 170, 0);
Dialog.show()
projectName=Dialog.getString();
counterstainingChannel=Dialog.getChoice();
trackerChannel=Dialog.getChoice();
maximumRadius=Dialog.getNumber();
thresholdCounterstain=Dialog.getNumber();
prominence=Dialog.getNumber();
thresholdTracker=Dialog.getNumber();
minSize=Dialog.getNumber();
// check the parameter selection
if(counterstainingChannel==trackerChannel) {
beep();
exit("Counterstaining ["+counterstainingChannel+"] and Tracker ["+trackerChannel+"] channels can not be the same")
}
// create a parameter dataset file
title1 = "Parameter dataset";
title2 = "["+title1+"]";
f = title2;
run("Table...", "name="+title2+" width=500 height=500");
print(f, "Project\t" + projectName);
print(f, "Counterstaining channel\t" + counterstainingChannel);
print(f, "Tracker channel\t" + trackerChannel);
print(f, "Maximum (radius)\t" + maximumRadius);
print(f, "Threshold (counterstain)\t" + thresholdCounterstain);
print(f, "Prominence >\t" + prominence);
print(f, "Threshold (tracker)\t" + thresholdTracker);
print(f, "Min object size\t" +minSize);
// save as txt
saveAs("txt", dir+File.separator+projectName);
selectWindow(title1);
run("Close");
// create an array containing the well codes
for (i=0; i1) {
getDimensions(widthTracker, heightTracker, channelsTracker, slicesTracker, framesTracker);
newImage("Seeds", "8-bit white", widthTracker, heightTracker, 1);
for (k=0; k1) {
getDimensions(widthTracker, heightTracker, channelsTracker, slicesTracker, framesTracker);
newImage("Seeds", "8-bit white", widthTracker, heightTracker, 1);
for (k=0; k