/*
ZFBONE - Version 1.1
DEVELOPERS: Marco Tarasco & Fabrice Cordelières
EMAIL: marcotar90@gmail.com & fabrice.cordelieres@u-bordeaux.fr
LAST EDITED: September 4th,2020
*/
macro "ZFBONE Action Tool - C012D00D01D02D06D08D09D10D13D15D16D20D23D24D25D30D37D40D43D50D55D56D57D60D64D65D67D70D71D72D74D77D79D80D81D82D84D85D86D87D89D90Da0Db0Db3Db6Db7Db8Db9Dc0Dc6Dd0Dd3Dd4Dd5Dd6De0De3Df0Df1Df2Cf00D11D12D17D18D19D21D22D26D27D28D29D31D32D35D36D38D39D41D42D44D45D48D49D51D52D53D54D58D59D61D62D63D68D69D91D92D93D94D95D96D97D98D99Da1Da2Da3Da4Da5Da6Da7Da8Da9Db1Db2Db4Db5Dc1Dc2Dc4Dc5Dd1Dd2De1De2C112D03D07D33D34D46D47D73D78D83D88Dc3Df3CfffD0aD1aD1cD1dD1eD2aD2cD2eD3aD3dD4aD4bD4cD4dD4eD4fD5aD6aD6cD6dD6eD7aD8aD8bD8cD8dD8eD8fD9aDaaDabDadDaeDafDbaDbbDbcDbeDbfDcaDdaDdbDdcDddDdeDdfDeaDfaDfcDfeC000C02fD0bD0cD0dD0eD0fD1bD1fD2bD2dD2fD3bD3cD3eD3fD5bD5cD5dD5eD5fD6bD6fD7bD7cD7dD7eD7fD9bD9cD9dD9eD9fDacDbdDcbDccDcdDceDcfDebDecDedDeeDefDfbDfdDff"{
infoAbout();
}
function infoAbout(){
bioskelLink="http://bioskel.ccmar.ualg.pt/";
bioskelIcon="http://bioskel.ccmar.ualg.pt/images/bioskel.png";
bicLink="http://www.bic.u-bordeaux.fr/";
bicIcon="https://upload.wikimedia.org/wikipedia/commons/4/44/Logo_BIC.png";
neubiasLink="http://eubias.org/NEUBIAS/";
neubiasIcon="http://eubias.org/NEUBIAS/wp-content/uploads/2016/07/Logo36-300x159.png";
GitHub="https://github.com/MarcoTarasco/ZFBONE";
html=""
+""
+"ZFBONE
"
+""
+"Developed by:"
+"
"
+"
Marco Tarasco (marcotar90@gmail.com)"
+"
Fabrice Cordelières (fabrice.cordelieres@u-bordeaux.fr)"
+"
"
+"
"
+"Version 1.1 "
+"LAST EDITED: September 4th, 2020 "
+"
"
+"Please check our page for updates and video tutorials on "
+"GitHub"
+"
"
+"
"
+"We acknowledge NEUBIAS: Network of European BioImage Analysts, COST Action CA15124"
+"
"
+"
"
+""
+""
+iconAndLink(bioskelLink, bioskelIcon, 154, 128)
+iconAndLink(neubiasLink, neubiasIcon, 150, 80)
+iconAndLink(bicLink, bicIcon, 158, 57)
+""
+""
+"";
showMessage("About...", html);
}
//----------------------------------------------------------------------------------
function iconAndLink(urlLink, urlIcon, width, height){
img="![\"There](\""+urlIcon+"\")
";
code=""+img+"";
return code;
}
//------------------------------------------OPERCULUM MACRO--------------------------------------------------//
macro "Operculum assay Action Tool - C000D17D26D27D28D29D35D38D39D3aD45D4bD54D5bD63D6cD73D76D77D7cD82D86D87D8dD92D9dDa2DadDb2DbdDc2DcdDd2DddDe2DedDf2DfdCf00Db5DbbDc5Dc6DcbDd6Dd7Dd8Dd9DdaDdbDe7De8De9DeaDf9"{
//Menu options
Dialog.create("Operculum assay");
Dialog.addRadioButtonGroup("Mode", newArray("Single","Batch"),1, 2, "Single");
Dialog.addRadioButtonGroup("Adjust contrast", newArray("Yes","No"),1, 2, "Yes");
Dialog.setInsets(5, 0, 0);
Dialog.addNumber("Set contrast value (0-10)", 2);
Dialog.addRadioButtonGroup("Number of channels (Ch) to analyze", newArray("1","2"),1, 2, "1");
Dialog.addRadioButtonGroup("Apply threshold in Ch1", newArray("Yes","No"),1, 2, "No");
Dialog.addRadioButtonGroup("Apply threshold in Ch2", newArray("Yes","No"),1, 2, "Yes");
Dialog.setInsets(5, 10, 0);
Dialog.addRadioButtonGroup("Threshold", newArray("Interactive","Not interactive"),1, 2, "Interactive");
Dialog.setInsets(5, 10, 0);
Dialog.addNumber("Set threshold Ch1 (0-255)*", 0);
Dialog.setInsets(5, 10, 0);
Dialog.addNumber("Set threshold Ch2 (0-255)*", 0);
Dialog.setInsets(5, 10, 0);
Dialog.addMessage("* Threshold min value depends on \nimage aquisition parameters");
Dialog.addRadioButtonGroup("Measure head area", newArray("Yes","No"),1, 2, "Yes");
// Dialog.addMessage(" ");
Dialog.setInsets(5, 10, 0);
Dialog.addMessage("Set measurements");
Dialog.setInsets(5, 20, 0);
Dialog.addCheckboxGroup(1, 2, newArray("Area","Intensity"), newArray(true,false));
//Help message
//------
UserManualOperculum="https://github.com/MarcoTarasco/ZFBONE#operculum-assay-";
html = ""
+"Operculum assay
"
+"Please check the online manual and video tutorial available on "
+"GitHub"
//Get user choices from menu
Dialog.addHelp(html);
Dialog.show();
mode=Dialog.getRadioButton();
Applycontrast=Dialog.getRadioButton();
contrastValue=Dialog.getNumber();
channel=Dialog.getRadioButton();
applyThreshold1=Dialog.getRadioButton();
applyThreshold2=Dialog.getRadioButton();
ThresholdMode=Dialog.getRadioButton();
nCh1=Dialog.getNumber();//threshold min value channel 1
nCh2=Dialog.getNumber();//threshold min value channel 2
UseHead=Dialog.getRadioButton();
ShowOpArea=Dialog.getCheckbox();
ShowInt=Dialog.getCheckbox();
// analyse single image or batch?
if (mode=="Single") {
doAnalysis();
}
else {
dir=getDirectory("Choose a Directory");
list=getFileList(dir);
for (i = 0; i < list.length; i++) {
if (endsWith(toLowerCase(list[i]), ".bmp")||endsWith(toLowerCase(list[i]), ".tif")||endsWith(toLowerCase(list[i]), ".jpg")){
if(!File.exists(dir+"analyzed/"+list[i]+"_analyzed.jpg")){
open(dir+list[i]);
doAnalysis();
run("Close All");
}
}
}
}
function doAnalysis(){
if (channel=="1") {
if (nImages==0) waitForUser("Please open an image (1 channel)");
if (nImages==0) exit("No image was opened!!");
}
else {
if (nImages==0) waitForUser("Please open an image (2 channel)");
if (nImages==0) exit("No image was opened!!");
}
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
roiManager("reset");
roiManager("Show None");
dir=getDirectory("image");
img=getTitle();
// adjust contrast?
autoContrast();
// Are you measuring the head area?
if (UseHead=="Yes") {
areaHead=getRoiMeasure("polygon", "Head");
}
// Decide if you work with 1 channel or 2
if (channel=="1") {
setTool("freehand");
while(selectionType==-1){
waitForUser("Select "+"Operculum area Ch1");
}
roiManager("Add");
List.setMeasurements;
areaOperculum=List.getValue("Area");
getRawStatistics(nPixels, mean, min, max, std, histogram);
TOtIntensity=nPixels*mean;
if (applyThreshold1=="Yes") {
thr1Ch=colorThresholding1Ch();
run("Restore Selection");
List.setMeasurements;
OpChOneFluoArea=List.getValue("RawIntDen")/255;
run("Create Selection");
roiManager("add");
}
setResult("Label", nResults, img);
// if the head was measured show ratio
if (UseHead=="Yes") {
Ratio=areaOperculum/areaHead;
setResult("Hd area", nResults-1, areaHead);
}
if (ShowOpArea==true) setResult("Op area Ch1", nResults-1, areaOperculum);
if (UseHead=="Yes") {
setResult("Op/Hd Ch1", nResults-1, Ratio);
}
if (ShowInt==true)setResult("Signal intensity Ch1", nResults-1, TOtIntensity);
if (applyThreshold1=="Yes") {
setResult("Signal area Ch1", nResults-1, OpChOneFluoArea);
if (ShowInt==true)setResult("Signal intensity Ch1", nResults-1, TOtIntensity);
setResult("MIN Thr Ch1", nResults-1, thr1Ch[0]);
setResult("MAX Thr Ch1", nResults-1, thr1Ch[1]);
}
//Rename and color ROIs
if (UseHead=="Yes") {
roiManager("Select", 0);
roiManager("Set Color", "magenta");
roiManager("Rename", "Head area");
roiManager("Select", 1);
roiManager("Set Color", "blue");
roiManager("Rename", "Operculum area");
if (applyThreshold1=="Yes") {
roiManager("select", newArray(1,2));
roiManager("AND");
roiManager("add");
roiManager("Select", 3);
roiManager("Set Color", "red");
roiManager("Rename", "Op signal Ch1");
roiManager("deselect");
roiManager("select", 2);
roiManager("delete");
}
}
else {
roiManager("Select", 0);
roiManager("Set Color", "red");
roiManager("Rename", "Operculum area");
roiManager("Show All without labels");
if (applyThreshold1=="Yes") {
roiManager("select", newArray(0,1));
roiManager("AND");
roiManager("add");
roiManager("Select", 2);
roiManager("Set Color", "red");
roiManager("Rename", "Op signal Ch1");
roiManager("select", 1);
roiManager("delete");
}
}
}
// the user choose to work with 2 channels
else {
if (nImages==0) waitForUser("Please open an image (2 channel)");
if (nImages==0) exit("No image was opened!!");
run("Labels...", "color=white font=12 show use");
selectWindow(img);
run("8-bit");
run("Split Channels");
selectWindow("C1-"+img);
setTool("freehand");
while(selectionType==-1){
waitForUser("Select Operculum area Ch1");
}
List.setMeasurements;
OpChOneArea=List.getValue("Area");
getRawStatistics(nPixels, mean, min, max, std, histogram);
OpChOneMeanIntensity=nPixels*mean;
if (UseHead=="Yes") {
Ratio=OpChOneArea/areaHead;
}
roiManager("add");
if (UseHead=="Yes") {
roiManager("Select", 0);
roiManager("Set Color", "magenta");
roiManager("Rename", "Head area");
roiManager("Select", 1);
roiManager("Set Color", "blue");
roiManager("Rename", "Op area Ch1");
}
else {
roiManager("Select", 0);
roiManager("Set Color", "blue");
roiManager("Rename", "Op area Ch1");
}
getRawStatistics(nPixels, mean, min, max, std, histogram);
OpChOneMeanIntensity=nPixels*mean;
//run("Select None");
if (applyThreshold1=="Yes") {
thr1Ch=colorThresholding1Ch();
run("Restore Selection");
List.setMeasurements;
OpChOneFluoArea=List.getValue("RawIntDen")/255;
run("Create Selection");
roiManager("add");
if (UseHead=="Yes") {
roiManager("Select", 2);
roiManager("Set Color", "blue");
roiManager("Rename", "Op signal Ch1");
}
else {
roiManager("Select", 1);
roiManager("Set Color", "blue");
roiManager("Rename", "Op signal Ch1");
}
}
// work on the second channel
selectWindow("C2-"+img);
if (UseHead=="Yes") {
roiManager("Select", 1);
}
else {
roiManager("Select", 0);
}
getRawStatistics(nPixels, mean, min, max, std, histogram);
OpChTwoMeanIntensity=nPixels*mean;
selectWindow("C2-"+img);
if (applyThreshold2=="Yes") {
thr2Ch=colorThresholding2Ch();
run("Restore Selection");
List.setMeasurements;
OpChTwoFluoArea=List.getValue("RawIntDen")/255;
run("Create Selection");
roiManager("add");
if (UseHead=="Yes") {
roiManager("Select", 2);
roiManager("Set Color", "yellow");
roiManager("Rename", "Op signal Ch2");
}
else {
roiManager("Select", 1);
roiManager("Set Color", "yellow");
roiManager("Rename", "Op signal Ch2");
}
}
//Organize ROIs
if (applyThreshold1=="Yes" && applyThreshold2=="Yes") {
if (UseHead=="Yes") {
roiManager("select", newArray(1,2));
roiManager("AND");
roiManager("add");
roiManager("Select", 4);
roiManager("Set Color", "red");
roiManager("Rename", "Op signal Ch1");
roiManager("select", newArray(1,3));
roiManager("AND");
roiManager("add");
roiManager("Select", 5);
roiManager("Set Color", "green");
roiManager("Rename", "Op signal Ch2");
roiManager("Select", newArray(2,3));
roiManager("delete");
}
else {
roiManager("select", newArray(0,1));
roiManager("AND");
roiManager("add");
roiManager("Select", 2);
roiManager("Set Color", "red");
roiManager("Rename", "Op signal Ch1");
roiManager("select", newArray(0,2));
roiManager("AND");
roiManager("add");
roiManager("Select", 3);
roiManager("Set Color", "green");
roiManager("Rename", "Op signal Ch2");
roiManager("Select", newArray(1,2));
roiManager("delete");
roiManager("Select", 1);
roiManager("Set Color", "red");
roiManager("Rename", "Op signal Ch1");
roiManager("Select", 2);
roiManager("Set Color", "green");
roiManager("Rename", "Op signal Ch2");
}
}
if (applyThreshold1=="No" && applyThreshold2=="Yes") {
if (UseHead=="Yes") {
roiManager("select", newArray(1,2));
roiManager("AND");
roiManager("add");
roiManager("Select", 3);
roiManager("Set Color", "green");
roiManager("Rename", "Op signal Ch2");
roiManager("select", 2);
roiManager("delete");
}
else {
roiManager("select", newArray(0,1));
roiManager("AND");
roiManager("add");
roiManager("Select", 2);
roiManager("Set Color", "green");
roiManager("Rename", "Op signal Ch2");
roiManager("select", 1);
roiManager("delete");
}
}
if (applyThreshold1=="Yes" && applyThreshold2=="No") {
if (UseHead=="Yes") {
roiManager("select", newArray(1,2));
roiManager("AND");
roiManager("add");
roiManager("Select", 3);
roiManager("Set Color", "red");
roiManager("Rename", "Op signal Ch1");
roiManager("select", 2);
roiManager("delete");
}
else {
roiManager("select", newArray(0,1));
roiManager("AND");
roiManager("add");
roiManager("Select", 2);
roiManager("Set Color", "red");
roiManager("Rename", "Op signal Ch1");
roiManager("select", 1);
roiManager("delete");
}
}
//Set result table
setResult("Label", nResults, img);
if (UseHead=="Yes") {
setResult("Head area", nResults-1, areaHead);
}
setResult("Op area 1Ch", nResults-1, OpChOneArea);
if (applyThreshold1=="Yes") {
setResult("Signal area Ch1", nResults-1, OpChOneFluoArea);
if (UseHead=="Yes") {
setResult("Op/Hd Ch1", nResults-1, Ratio);
}
if (ShowInt==true){
setResult("Signal intensity Ch1", nResults-1, OpChOneMeanIntensity);
}
setResult("MIN Thr Ch1", nResults-1, thr1Ch[0]);
setResult("MAX Thr Ch1", nResults-1, thr1Ch[1]);
}
if (applyThreshold2=="Yes") {
if (UseHead=="Yes") {
setResult("Op/Hd Ch1", nResults-1, Ratio);
}
setResult("Signal area Ch2", nResults-1, OpChTwoFluoArea);
if (ShowInt==true){
setResult("Signal intensity Ch2", nResults-1, OpChTwoMeanIntensity);
}
setResult("MIN Thr Ch2", nResults-1, thr2Ch[0]);
setResult("MAX Thr Ch2", nResults-1, thr2Ch[1]);
}
}
if (channel=="2") {
open(dir+img);
run("Make Composite");
run("Stack to RGB");
selectWindow(img+" (RGB)");
}
if (channel=="1" && applyThreshold1=="Yes"){
open(dir+img);
}
roiManager("Deselect");
roiManager("Show All");
run("Flatten");
getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
dateTag=""+year+"-"+IJ.pad((month+1), 2)+"-"+IJ.pad((dayOfMonth), 2)+"_"; // now it is saving with the day fo the month wrong.. should i remove +1?
direct=dir+"analyzed/";
File.makeDirectory(direct);
roiManager("Save",direct+img+"_RoiSet.zip");
saveAs("jpeg",direct+img+"_analyzed");
Table.save(direct+dateTag+"_Operculum_Results.xls");
run("Close All");
}
//------------------------------------
function getRoiMeasure(tool, name){
setTool(tool);
while(selectionType==-1){
waitForUser("Select "+name+" area");
}
roiManager("Add");
getStatistics(area, mean, min, max, std, histogram);
run("Select None");
return area;
}
//------------------auto contrast---------------------------//
function autoContrast(){
run("8-bit");
if(Applycontrast=="Yes"){
getStatistics(area, mean, min, max, std, histogram);
setMinAndMax(maxOf(mean-contrastValue*std, min), minOf(mean+contrastValue*std, max));
run("Apply LUT");
}
}
//------------------Threshold functions---------------------------//
function colorThresholding1Ch(){
run("Enhance Contrast", "saturated=0.35");
if (ThresholdMode=="Not interactive"){
setThreshold(nCh1, 255);
}
else {
setAutoThreshold("IJ_IsoData dark");
}
run("Threshold...");
setOption("BlackBackground", false);
if (ThresholdMode=="Interactive"){
waitForUser("Adjust threshold Ch1, then press Ok");
}
getThreshold(lower, upper);
run("Convert to Mask");
return newArray(lower,upper);
}
function colorThresholding2Ch(){
run("Enhance Contrast", "saturated=0.35");
if (ThresholdMode=="Not interactive"){
setThreshold(nCh2, 255);
}
else {
setAutoThreshold("Triangle dark");
}
setOption("BlackBackground", false);
run("Threshold...");
if (ThresholdMode=="Interactive") waitForUser("Adjust threshold Ch2, then press Ok");
getThreshold(lower, upper);
run("Convert to Mask");
return newArray(lower,upper);
}
}
}
}
//------------------------------------------SCALES ASSAY--------------------------------------------------//
macro "Scale assay Action Tool - C000D02D0dD12D1dD22D2dD31D32D3dD3eD40D42D4dD4fD50D52D5dD5fD60D61D62D6dD6fD70D72D7dD7fD82D8dD8eD92D9dDa2DadDb2DbdDc2DcdDd2DddDe3De4DebDecDf3Df4DfbDfcCf00D03D05D07D09D0bD13D15D16D17D19D1aD1bD34D36D38D3aD3cD44D45D46D48D49D4aD4cD64D66D68D6aD6cD73D74D76D77D78D7aD7bD7cD93D95D97D99D9bDa3Da4Da5Da7Da8Da9DabDacDc4Dc6Dc8DcaDccDd4Dd5Dd6Dd8Dd9DdaDdcDf6Df8Dfa"{
//-------------------------------user menu setup-------------------------
Dialog.create("Scale assay");
Dialog.setInsets(0, 1, 0);
Dialog.addRadioButtonGroup("Staining", newArray("TRAP","von Kossa"),1, 2, "TRAP");
Dialog.setInsets(0, 1, 0);
Dialog.addRadioButtonGroup("Mode", newArray("Single","Batch"),1, 2, "Single");
Dialog.setInsets(0, 1, 0);
Dialog.addRadioButtonGroup("Threshold", newArray("Interactive","Not interactive"),1, 2, "Interactive");
Dialog.setInsets(0, 1, 0);
Dialog.addMessage(" ");
Dialog.setInsets(0, 1, 0);
Dialog.addNumber("Set threshold (0-255)*", 165);
Dialog.setInsets(0, 1, 0);
Dialog.addMessage("* Threshold min value depends on \nimage aquisition parameters");
//------
UserManualScales="https://github.com/MarcoTarasco/ZFBONE#scales-assay-";
html = ""
+"Scale assay
"
+"Please check the online manual and video tutorial available on "
+"GitHub"
//------
Dialog.addHelp(html);
Dialog.show();
assay=Dialog.getRadioButton();
mode=Dialog.getRadioButton();
analysis=Dialog.getRadioButton();
numbtr=Dialog.getNumber();
if (mode=="Single") {
if (nImages==0) waitForUser("Open an image!!");
if (nImages==0) exit("No image was opened...");
if (bitDepth()!=24) exit("Open an RGB image!!");
img=getTitle();
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
dir=getDirectory("image");
dark=(assay=="TRAP");
getROI();
thr=process(dark);
table();
measureAndTable(dark, thr);
SaveOutput(dark, dir, img);
}
else {
dir=getDirectory("Choose a Directory");
list=getFileList(dir);
if(!File.exists(dir+"analyzed/")){
for (i = 0; i < list.length; i++) {
if (endsWith(toLowerCase(list[i]), ".bmp")||endsWith(toLowerCase(list[i]), ".tif")){
open(dir+list[i]);
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
img=getTitle();
dir=getDirectory("image");
dark=(assay=="TRAP");
getROI();
thr=process(dark);//will give true or false
table();
measureAndTable(dark, thr);//will give true or false
SaveOutput(dark, dir, img);
}
}
}
else {
exit("Analyses already done!!");
}
}
}
//------------------------------------------------------------------------------------------
function getROI(){
roiManager("reset");
run("Select None");
while(roiManager("count")==0){
setTool("polygon");
waitForUser("Select scale area, then type (T) \nto add it in the ROI manager");
}
for (i=0;i=2){
roiManager("Combine");
}
else {
roiManager("select", 0);
}
arg=" exclude";
if(isTrap) arg="";
run("Analyze Particles...", arg+" show=Masks");
if(!isTrap){
return THRVKossa;
}
else {
return THRTraP;
}
}
//----------------------------------------
function VonKossaThreshold() {
run("8-bit");
run("Enhance Contrast", "saturated=0.35");
setThreshold(numbtr, 255);
run("Threshold...");
//setAutoThreshold("MaxEntropy dark");
if (analysis=="Interactive"){
setAutoThreshold("MaxEntropy dark");
waitForUser("Adjust threshold, then press Ok");
}
getThreshold(lower, upper);
run("Convert to Mask");
return newArray(lower,upper);
}
function TrapThreshold(){
min=newArray(3);
max=newArray(3);
filter=newArray(3);
img=getTitle();
call("ij.plugin.frame.ColorThresholder.RGBtoYUV");
run("RGB Stack");
run("Convert Stack to Images");
selectWindow("Red");
rename("0");
selectWindow("Green");
rename("1");
selectWindow("Blue");
rename("2");
min[0]=0;
max[0]=255;
filter[0]="pass";
min[1]=0;
max[1]=255;
filter[1]="pass";
min[2]=numbtr;
max[2]=255;
filter[2]="pass";
selectWindow("2");
run("Threshold...");
setThreshold(min[2], max[2]);
if (analysis=="Interactive"){
setAutoThreshold("MaxEntropy dark");
waitForUser("Adjust threshold, then press Ok");
}
getThreshold(lower, upper);
for (i=0;i<3;i++){
selectWindow(""+i);
setThreshold(min[i], max[i]);
run("Convert to Mask");
if (filter[i]=="stop") run("Invert");
}
imageCalculator("AND create", "0","1");
imageCalculator("AND create", "Result of 0","2");
for (i=0;i<3;i++){
selectWindow(""+i);
close();
}
selectWindow("Result of 0");
close();
selectWindow("Result of Result of 0");
rename(img);
return newArray(lower,upper);
}
//------------------------------------------------------------------------------------------
function measureAndTable(isTRAP, thr){
img=replace(getTitle(), "Mask of ", "");
roiManager("Show All with labels");
roiManager("UseNames", "true");
for (i=0;iCaudal fin assay"
+"Please check the online manual and video tutorial available on "
+"GitHub"
//------
Dialog.addHelp(html);
Dialog.show();
assay= Dialog.getRadioButton();
ThresholdMode=Dialog.getRadioButton();
FinThr=Dialog.getNumber();
if (assay=="Bone mineralization (MIN)") Caudalfin();
if (assay=="Ray morphometrics (MORP)") Raymorphometrics();
if (assay=="MIN & MORP") Both();
if (assay=="TRAP signal") TRAPassay();
}
//------------------------------------------------------
function Caudalfin() {
roiManager("reset");
waitForUser("Open Brightfield image");
if (nImages==0) exit("Open an image!!");
brightfield=getTitle();
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
waitForUser("Open fluorescence image");
if (nImages==0) exit("Open an image!!");
fluorescence=getTitle();
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
path=getDirectory("image")+fluorescence;
run("Labels...", "color=white font=12 show use");
run("Line Width...", "line=1");
setTool("line");
selectWindow(brightfield);
if(bitDepth()==24) run("16-bit");
while(selectionType==-1){
waitForUser("Select STU");
}
List.setMeasurements;
Stu=List.getValue("Length");
roiManager("Add");
roiManager("Select", 0);
roiManager("Set Color", "yellow");
roiManager("Set Line Width", 3);
roiManager("Rename", "STU");
roiManager("Show All without labels");
roiManager("UseNames", "true");
setTool("polygon");
selectWindow(brightfield);
while(selectionType==-1){
waitForUser("Select REG");
}
List.setMeasurements;
Reg=List.getValue("Area");
roiManager("Add");
roiManager("Select", 1);
roiManager("Set Color", "blue");
roiManager("Rename", "REG");
//Pass to rays measuraments
setTool("line");
run("Select None");
while(selectionType==-1){
waitForUser("Select RAY, then type (T) to add it to the ROI manager");
}
//i starts at 2 to avoid measuring the first ROIs which are the STU, REG ROI
Ray=0;
for (i=2;iRay bone intensity assay"
+"Please check the online manual and video tutorial available on "
+"GitHub"
//------
Dialog.addHelp(html);
Dialog.show();
assay=Dialog.getRadioButton();
if (assay=="Ray analysis") {
run ("RayAnalysis");
}
else {
run ("Data pooling");
}
}
macro "RayAnalysis" {
cleanUp();
if (nImages==0) waitForUser("Open an image!!");
if (nImages==0) exit("No image was opened...");
img=getTitle();
askForROIs();
maxArray=getData();
maxPosition=shiftColumns(maxArray);
normalize(maxPosition);
generateXValues();
fillEmptyCells();
plotShiftedNormalized(true);
generateOutput(img);
saveEverything(img);
run ("Close All");
//---------------------------------------------
function cleanUp(){
run("Clear Results");
roiManager("Reset");
roiManager("UseNames", "true");
close("All your data*");//close any window that has this name
}
//---------------------------------------------
function askForROIs(){
roiManager("Show All");
run("Line Width...", "line=30");
setTool("polyline");
waitForUser("Select each ray,then type (T) to add it to the ROI manager");
for(i=0; imax){
position=i;
max=inputArray[i];
}
}
return newArray(position, max);
}
//Then we shift all the data of each ray to start at the same point (max intensity)
function shiftColumns(maxArray){
Array.getStatistics(maxArray, min, maxOfMax, mean, stdDev);
for(i=0; imax){
position=i;
max=inputArray[i];
}
}
return newArray(position, max);
}
//Then we shift all the data of each ray to start at the same point (max intensity)
function shiftColumns(maxArray){
Array.getStatistics(maxArray, min, maxOfMax, mean, stdDev);
headers=split(Table.headings, "\t");
index=0;
for(i=0; i