/*
* Cell_Proliferation
* Authors: Pau Carrillo-Barberà, José M. Morante-Redolat, José F. Pertusa
* Department of Cellular & Functional Biology
* University of Valencia (Valencia, Spain)
*/
/*
* This macro is a high-throughput screening tool for cell proliferation assays.
* It is based on nucleoside analogue pulse alone or in combination with up to
* two additional nuclear markers.
*/
macro "Cell_Proliferation" {
//choose a macro mode and a directory
#@ String (label=" ", value="High Content Screening
Cell Proliferation", visibility=MESSAGE, persist=false) heading
#@ String(label="Select mode:", choices={"Analysis", "Pre-Analysis (parameter tweaking)"}, style="radioButtonVertical") mode
#@ File(label="Select a directory:", style="directory") dir
#@ String (label="Project", choices={"Filtering", "StarDist", "Load"}, persist=true, style="radioButtonHorizontal") project
#@ String (label="Load function", choices={"No", "Yes"}, value="Yes", persist=true, style="radioButtonHorizontal") illumCorr
#@ 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 (Spain)", visibility=MESSAGE, persist=false) message
//set options
setOption("ExpandableArrays", true);
setOption("BlackBackground", false);
setOption("ScaleConversions", true);
roiManager("reset");
print("\\Clear");
run("Clear Results");
close("*");
//File management
//Identification of the TIF files
//create an array containing the names of the files in the directory path
list = getFileList(dir);
Array.sort(list);
tifFiles=0;
//count the number of TIF files
for (i=0; idocumentation"
+" for help";
Dialog.addHelp(html);
Dialog.show()
projectName=Dialog.getString();
pattern[0]=Dialog.getChoice();
pattern[1]=Dialog.getChoice();
pattern[2]=Dialog.getChoice();
pattern[3]=Dialog.getChoice();
if (project == "Filtering") {
normalize=Dialog.getCheckbox();
gaussianNuclei=Dialog.getNumber();
thresholdNuclei=Dialog.getChoice();
erodeNuclei=Dialog.getNumber();
openNuclei=Dialog.getNumber();
watershedNuclei=Dialog.getCheckbox();
} else {
overlap_threshold=Dialog.getNumber();
}
size=Dialog.getString();
flat_field[0]=Dialog.getChoice();
flat_field[1]=Dialog.getChoice();
flat_field[2]=Dialog.getChoice();
flat_field[3]=Dialog.getChoice();
if (pattern[2]=="Empty" && pattern[3] != "Empty") {
pattern[2]=pattern[3];
pattern[3]="Empty";
flat_field[2]=flat_field[3];
flat_field[3]="None";
}
pattern_fullname=newArray("Empty", "Empty", "Empty", "Empty");
for (i=0; i=10) {
maxRandomFields=10;
} else {
maxRandomFields=fieldsxwell;
}
Dialog.addMessage("Random fields per well:");
Dialog.addSlider("", 1, maxRandomFields, maxRandomFields);
measurements=newArray("Area", "Circ.", "AR", "Solidity", "Round", "Mean", "IntDen");
Dialog.addChoice("Measure", measurements, "Mean");
Dialog.addNumber("Split threshold", 250);
Dialog.addNumber("Set Line Width", 3);
}
Dialog.addHelp(html);
Dialog.show();
selectionMode=Dialog.getRadioButton();
if(mode=="Pre-Analysis (parameter tweaking)") {
maxRandomFields=Dialog.getNumber();
measure_test=Dialog.getChoice();
split_test=Dialog.getNumber();
roi_line_width=Dialog.getNumber();
}
for (i=0; i=0; i--) {
if (number==randomArray[i]) {
recurrent=true;
}
}
if(recurrent==false || count==0) {
// open images
channels_test=newArray(2);
for (i=0; i max) {
roiDiscard[discardCount]=i;
discardCount++;
}
}
if (discardCount != 0) {
roiManager("select", roiDiscard);
roiManager("delete");
}
run("Clear Results");
}
function excludeEdges() {
roiEdge=newArray();
run("Set Measurements...", "bounding display redirect=None decimal=2");
roiManager("deselect");
roiManager("measure");
nROI=roiManager("count");
getDimensions(width, height, channels, slices, frames);
toScaled(width);
toScaled(height);
roiEdgeCount=0;
for (i=0; i= width || by + iHeight >= height) {
roiEdge[roiEdgeCount]=i;
roiEdgeCount++;
}
}
if (roiEdgeCount != 0) {
roiManager("select", roiEdge);
roiManager("delete");
}
run("Clear Results");
}
function displayOutlines (image1, image2, getMeasure, threshold, line_width) {
index1=indexOf(image1, "(");
index2=indexOf(image1, " wv");
well=substring(image1, 0, index1)+ ")";
field=substring(image1, index1, index2)+ ")";
name=well + " " +field;
run("Merge Channels...", "c1=["+image2+"] c3=["+image1+"] keep");
rename(name);
run("Set Measurements...", "area mean shape integrated display redirect=["+image2+"] decimal=2");
roiManager("deselect");
roiManager("measure");
nROI=roiManager("count");
roiManager("Set Line Width", line_width);
for (a=0; a threshold) {
roiManager("select", a);
roiManager("Set Color", "orange");
roiManager("draw");
} else {
roiManager("select", a);
roiManager("Set Color", "cyan");
roiManager("draw");
}
}
}
function hours_minutes_seconds(seconds) {
hours=seconds/3600;
hours_floor=floor(hours);
remaining_seconds=seconds-(hours_floor*3600);
remaining_minutes=remaining_seconds/60;
minutes_floor=floor(remaining_minutes);
remaining_seconds=remaining_seconds-(minutes_floor*60);
hours_floor=d2s(hours_floor, 0);
minutes_floor=d2s(minutes_floor, 0);
remaining_seconds=d2s(remaining_seconds, 0);
if (lengthOf(hours_floor) < 2) hours_floor="0"+hours_floor;
if (lengthOf(minutes_floor) < 2) minutes_floor="0"+minutes_floor;
if (lengthOf(remaining_seconds) < 2) remaining_seconds="0"+remaining_seconds;
return hours_floor+":"+minutes_floor+":"+remaining_seconds;
}
}