Image J angiogenesis分析安装
1.首先你需要安装好一个可以运行的image j,然后你会发现有的你需要的功能需要自己下载插件。
2.然后https://imagej.nih.gov/ij/plugins/index.html这个网址下载你需要的插件。打开toolsets或者tools,因为我是做成血管结果分析所以我需要的插件在toolsets里。按照如下步骤复制所需插件的内容，自己建立一个txt. 文档。
3.打开image j,单击顶部plugins-new-macro,复制之前的txt内容到打开的空白界面
4.在Macros的页面里, 选择macros-install macros。然后就装好啦！！！！
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// Angiogenesis Analyzer
// Author : Gilles Carpentier
// Faculte des Sciences et Technologie,
// Universite Paris Est Creteil Val de Marne, France.
var mapJunctionID=0, mapSegmentID=0, mapBranchID=0, mapMasterJunctionID=0;
var initid=0,workid=0,workingima="",mapExtremaID=0,mapNodesID=0,starttime,q3id,excludeObjectsSize=10,seconds=0;
var twigSize=25,nbExtrema=0,nbNodes=0,nbJunctions=0,nbLoop=0,nbTwigs,nbSegments,nbIsolated,nbTotalPeaces,loopSize=850, seuilIsolFinal=25,showLoopInBlue=0;
var nbMesh=0, totalMeshSize=0, initSkeleton=0;
var totalLenght=0, totalSegmentsLenght=0, totalTwigsLenght=0, totalBranchingLenght=0,totalIsolatedLenght=0,analyzedArea=0,branchingIndex=0,meshIndex=0,meanMeshSize=0;
var findloopOption=1,pass=0,supressTwig =1,supressIsolated=0,showSupressIsolated=1,nbIt=3;
var TwigID,showOnlyFinal=1,showLoops=0,showMesh=1,showNodes=1,showExtrema=1,showTwig=1,showMasterSegments=1,showSegments=1,showIsolated=1,showPassChoice=3,rmspeckles=1,Speckelradius=5;
var supressVerySmallSegments=1,smoothEachLimbing=1; // state = 1 required for ImageJ skeletonize function
var supressSmallSegments=1, sizeExcludeSegments=30;
var finalmapBigNodesID=0, smootMapID=0;
var recordStepOption=0, step=1, stepByStep=0;
var analyseMasterTree=1, masterTreeID=0, mapMasterTreeID=0, nbMasterJunctions=0, nbMasterJunctionsFinal=0, nbMasterSgment=0, totalMasterSegmentLenght=0;
var singleAnaMapExtID=0, singleAnaMapNodeID=0, singleShowMaps=0;
// variable for tab part
var windowTabName="Stat Results Table",nameOfStatTab="["+windowTabName+"]",label="",undoErease="",batchChoice=0,imageFolder="",nameInitImageorFolder="";
var objectsChoices= newArray ("Analyze HUVEC Phase Contrast","Analyze HUVEC Fluo"), objectsChoice="Analyze HUVEC Phase Contrast", objects=0, excludeIlandsSize = 20;
var menuChoices= newArray ("-","Analyze Binary Tree","-","Save Current Analysis" , "Close Current Analysis","Save Current Analysis and Close","-","Blink Overlay [b]","Hide Overlay [h]","Show Overlay [s]");
var TreatedFolderSuffix ="=AN/", treatedImageSuffix="", ext1=".tif",ext2=".TIF";
var batchStatus="[Batch Progress Window]", batchStatusWindow="Batch Progress Window",countBatchTreated=0,countBatch=0,starttime=0,fileProcessed="";
var ecranX=screenWidth, ecranY=screenHeight,onFoldeByImage=0,folderTreatedpath;
var sufficAn="-tr";
var segmentCoul = "#f00efc", branchCoul = "#23e500", extremityCoul= "#f70133", extremityEdgeCoul= "#f7eb00", junctionCoul="#0035ff", twigColour="#19e7fb", isolatedTwigCoul="#00f7fa";
var nodesCoul="#ff1303", masterJunctionCoul="#ff2d00", masterSegmentCoul="#ffd300", isolatedElementCoul="#0005fe", meshCoul="#06adfd";
var rebuiltMapId=0;
varreBuiltElements = newArray ("segment","branch","extremity","extremityEdge","junction","twig","isolatedTwig","nodes","masterJunction","masterSegment","isolatedElement","mesh");
varreBuiltChoices = newArray (12), reBuiltChoicesNames = newArray (12);
var errorNetMessage ="Error: ";
var urllist = "http://image.bio.methods.free.fr/ij/ijupdatetest/ListOfMacros.txt";// to check the internet access
var onlinedoclink = "http://image.bio.methods.free.fr/ImageJ/?Angiogenesis-Analyzer-for-ImageJ.html";
var demoimagelink1 = "http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Pseudo-Phase-Contrast.tif.zip";
var demoimagelink2 = "http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Fluo.tif.zip";
var demoimagename1 = "HUVEC-Pseudo-Phase-Contrast.tif";
var demoimagename2 = "HUVEC-Fluo.tif";
var xx = requires147d(); // check version at install time
function requires147d() {requires("1.47d"); return 0; }
var concatMenuChoices=Array.concat(objectsChoices,menuChoices);
var menuanalysis=0;
var dCmds = newMenu("Network Analysis Menu Tool",concatMenuChoices);
macro "Network Analysis Menu Tool - C000D00D01D02D03D08D09D0aD0bD0cD0dD0eD0fD10D11D12D13D14D1aD1bD1cD1dD1eD20D21D22D23D24D2dD30D32D33D40D41D42D48D49D50D51D56D57D58D59D5fD66D67D68D6fD74D75D76D77D84D85D86D8cD90D96D9bD9cDa0DaaDabDacDadDb9DbaDbbDbcDbdDc0Dc1Dc2Dc3Dc8Dc9DcaDcbDccDceDd0Dd1Dd2Dd3Dd8Dd9DdaDdbDe0De1De2De8De9DeaDebDf0Df1Df2Df8Df9DfaDfbC002D69D83C000D31C573Dc6C212De7C021Dc7Cc84Da7C005Da9C001D18D5aDbeC0c8D5eC763D29Cdb0DafCa78D5dC004D07Dc4DcfC001D19D65D78D7fD87C695D7dC009D4fC430Dd7Cbf1D6bC015Db8C111DecC399D17C729D26Ccf0D4eCfffDddDdeDdfDedDeeDefDfdDfeDffC003D25D7cC000Db2C085D2eC007D94C050Db1Cbd5D82C006Da5C6a8D6cC269D97Cdb0Df4Cab6D06C012D95C6b6D93C02aDf5Ca91Df6Cfd2D89C017D2bD34C111DcdC1a9D46Cf38Db5Cee0D70C002D04D4aC685D81C034Dd6Ccc1D16C006D43D60D9aDe3C597D9fC216D2aCf87D71C686Da8C029D55DaeC640DbfCad4D6dC016D15C07bDf3Cf27D5cCdf0D3bC003D8bC000DfcC4f4D38C058D4bC070Db0Cfd2D98C8f6D39C53aDe6Ccc1D3fCac5D7eC024Da1Caf4D3aD3cC05aDf7C8c1D28Cff2D7aC017D80C6c8D8aCf69D27Cdf0D63C286D35C044D5bC005D2cD61C4d8D7bC555DdcC8a3Da4C029Db3Caf2D92C025D8dC598D53Ce4aD4cC395D6eC037Da6Cdd3Da3C9b6De4C26bD88Cca8Db6C014D47C8a6D9eC14aD79Cff1Dc5C0faD3dCf47D4dC576D62C136D91Cec2D45C697D99C349D6aCe8cD37C996Db4Cce3D8eC025D1fC29fDb7Cf27De5C004D52D9dC5f4D3eC168D64Cfd2D54C8f7D2fC36aDa2Ccf6Dd5C054Dd4C259D73Cef3D36C027D8fC8a8D44Cf2eD72C7b9D05"{
cmd = getArgument();
if (cmd!="-" && cmd != "Close Current Analysis" && cmd != "Save Current Analysis and Close" && cmd != "Save Current Analysis" && cmd != "Analyze Binary Tree" && cmd != "Blink Overlay [b]" && cmd != "Hide Overlay [h]" && cmd != "Show Overlay [s]") {
objectsChoice = cmd;
menuanalysis=1;
if (objectsChoice == objectsChoices[0]) objects = 1;
if (objectsChoice == objectsChoices[1]) objects = 2;
singleNetworkAnalysis ();
}
if (cmd!="-" && cmd == "Close Current Analysis") {closeAll ();}
if (cmd!="-" && cmd == "Save Current Analysis") {saveAndCloseAnalysis (0);}
if (cmd!="-" && cmd == "Save Current Analysis and Close") {saveAndCloseAnalysis (1);}
if (cmd!="-" && cmd == "Analyze Binary Tree") {analyseFromATree ();}
if (cmd!="-" && cmd == "Blink Overlay [b]") {blinkOverlay ();}
if (cmd!="-" && cmd == "Hide Overlay [h]") {run("Hide Overlay");}
if (cmd!="-" && cmd == "Show Overlay [s]") {run("Show Overlay");}
menuanalysis=0;
}
macro "Blurred Mask Action Tool - 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"{
setBatchMode(true);
imageTomask=getImageID();
if (selectionType() == -1) {
showMessage ("This tool requires a selection");
setTool("ellipse");
makeEllipse(30, 30, 100, 100, 0.4);
exit;
}
run("Select None");
run("Duplicate...", "title=masqueflou");
masqueflouID = getImageID();
run("Restore Selection");
run("Gaussian Blur...", "sigma=4");
run("Enlarge...", "enlarge=10");
run("Gaussian Blur...", "sigma=2");
run("Enlarge...", "enlarge=10");
run("Gaussian Blur...", "sigma=1");
run("Select None");
run("Select All");
run("Copy");
close();
selectImage(imageTomask);
setupUndo();
run("Paste");run("Select None");
}
var settingsMenuChoices= newArray ("Find a Tree","Find & Remove Loops","Find Extremities","Find Nodes and Junctions","Find Nodes and Branches","Record the Steps of Limbing","-","Get Maps of Selections","-","Blink Overlay [b]","Hide Overlay [h]","Show Overlay [s]","-","Settings");
var dCmds = newMenu("Tuning Functions Menu Tool",settingsMenuChoices);
macro "Tuning Functions Menu Tool - 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"{
cmd = getArgument();
if (cmd!="-" && cmd == "Find a Tree") {findTree ();}
if (cmd!="-" && cmd == "Find & Remove Loops") {FindAnfRemoveLoops ();}
if (cmd!="-" && cmd == "Find Extremities") {findExtremities ();}
if (cmd!="-" && cmd == "Find Nodes and Junctions") {findTheNodes ();}
if (cmd!="-" && cmd == "Find Nodes and Branches") {
findNodesAndBranches ();
setBatchMode("exit and display");
selectImage (workid);
}
if (cmd!="-" && cmd == "Get Maps of Selections") {getMapsOFSelections ();}
if (cmd!="-" && cmd == "Record the Steps of Limbing") {recordTheStepOfLimbing ();}
if (cmd!="-" && cmd == "Blink Overlay [b]") {blinkOverlay ();}
if (cmd!="-" && cmd == "Hide Overlay [h]") {run("Hide Overlay");}
if (cmd!="-" && cmd == "Show Overlay [s]") {run("Show Overlay");}
if (cmd!="-" && cmd == "Settings") {globalSettings ();}
}
macro "Batch Image Treatment Action Tool - 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"{
batchChoice=1;
batchProcessing ();
}
var ftabCmds = newMenu("Measurement Table Manager Menu Tool",newArray("Save a Stat Results Table","Save a Stat Results Table at the Image Location","-","Remove Last Table Line","Undo Remove Last Table Line", "-","Open a \"Stat Results Table\" Table File"));
macro "Measurement Table Manager Menu Tool - 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" {
cmd = getArgument();
if (cmd !="-" && cmd == "Save a Stat Results Table") {saveTab ("--",windowTabName,"");}
if (cmd !="-" && cmd == "Save a Stat Results Table at the Image Location") {saveTab (imageFolder,windowTabName,workingima);}
if (cmd !="-" && cmd == "Remove Last Table Line") {rmLastLine ();}
if (cmd !="-" && cmd == "Undo Remove Last Table Line") {undormLastLine ();}
if (cmd !="-" && cmd == "Open a \"Stat Results Table\" Table File") {openStatResultTable ();}
if (cmd !="-" && cmd == "Open a \"Stat Results Table\" Table File") {openStatResultTable ();}
if (cmd !="-" && cmd == "Open a \"Stat Results Table\" Table File") {openStatResultTable ();}
}
var dCmds = newMenu("Documentation & Demo Menu Tool",newArray ("Download a Pseudo Phase Contrast HUVEC Image","Download a Fluo HUVEC Image", "-", "Open On Line Documentation"));
macro "Documentation & Demo Menu Tool - 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"{
cmd = getArgument();
if (cmd!="-" && cmd == "Open On Line Documentation") {
doc ();
}
if (cmd!="-" && cmd == "Download a Pseudo Phase Contrast HUVEC Image") {
OpenImageLink(demoimagelink1,demoimagename1,1);
}
if (cmd!="-" && cmd == "Download a Fluo HUVEC Image") {
OpenImageLink(demoimagelink2,demoimagename2,1);
}
}
var dCmds = newMenu("Version and Update Information Menu Tool",newArray ("Version and Update Information", "About \"Angiogenesis Analyzer\""));
macro "Version and Update Information Menu Tool - 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" {
cmd = getArgument();
if (cmd == "Version and Update Information") {
VersionInfos ();
}
if (cmd == "About \"Angiogenesis Analyzer\"") {
aboutTheTools ();
}
}
//macro "About \"Angiogenesis Analyzer\" Action Tool - 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" {
//aboutTheTools ();
//}
function globalSettings () {
archtwigSize=twigSize;
archexcludeObjectsSize=excludeObjectsSize;
archloopSize = loopSize;
archseuilIsolFinal = seuilIsolFinal;
archsizeExcludeSegments = sizeExcludeSegments;
archnbIt = nbIt;
archshowPassChoice = showPassChoice;
alertMessage="";
listCheckBoxe1=newArray ("Show maps of elements \(single analysis\)","Show nodes and junctions","Show extremities","Show loops","Show meshes","Show branches","Show segments","Analyze master tree","Show master segments","Remove small master segments","Supress isolated elements","Show supressed isolated elements");
listCheckBoxesStatus=newArray ( lengthOf(listCheckBoxe1));
listCheckBoxesStatus[0]=singleShowMaps;
listCheckBoxesStatus[1]=showNodes;
listCheckBoxesStatus[2]=showExtrema;
listCheckBoxesStatus[3]=showLoops;
listCheckBoxesStatus[4]=showMesh;
listCheckBoxesStatus[5]=showTwig;
listCheckBoxesStatus[6]=showSegments;
listCheckBoxesStatus[7]=analyseMasterTree;
listCheckBoxesStatus[8]=showMasterSegments;
listCheckBoxesStatus[9]=supressSmallSegments;
listCheckBoxesStatus[10]=supressIsolated;
listCheckBoxesStatus[11]=showSupressIsolated;
testOK = 0;
while (testOK == 0) {
Dialog.create("Angiogenis Analyzer Settings");
Dialog.addMessage(alertMessage);
Dialog.addCheckboxGroup(4,4, listCheckBoxe1,listCheckBoxesStatus);
Dialog.addMessage("\n");
Dialog.addNumber("Minimum object size", excludeObjectsSize, 0, 3, "pixels");
Dialog.addNumber("Minimum branch size", twigSize, 0, 3, "pixels");
Dialog.addNumber("Artifactual loop size", loopSize, 0, 3, "pixels");
Dialog.addNumber("Isolated element size threshold", seuilIsolFinal, 0, 3, "pixels");
Dialog.addNumber("Master segment size threshold", sizeExcludeSegments, 0, 3, "pixels");
Dialog.addNumber("Iteration number \(advised 2 to 5\)", nbIt, 0, 3, "iteration\(s\)");
Dialog.addNumber("Show iteration \(for single analysis\)", showPassChoice, 0, 3, "iteration\(s\)");
html="http://image.bio.methods.free.fr/ImageJ/?Angiogenesis-Analyzer-for-ImageJ";
Dialog.addHelp(html);
Dialog.show();
alertMessage="";
singleShowMaps = Dialog.getCheckbox();
showNodes = Dialog.getCheckbox();
showExtrema = Dialog.getCheckbox();
showLoops = Dialog.getCheckbox();
showMesh = Dialog.getCheckbox();
showTwig = Dialog.getCheckbox();
showSegments = Dialog.getCheckbox();
analyseMasterTree = Dialog.getCheckbox();
showMasterSegments = Dialog.getCheckbox();
supressSmallSegments = Dialog.getCheckbox();
supressIsolated = Dialog.getCheckbox();
showSupressIsolated =Dialog.getCheckbox();
excludeObjectsSize = Dialog.getNumber();
twigSize = Dialog.getNumber();
loopSize = Dialog.getNumber();
seuilIsolFinal = Dialog.getNumber();
sizeExcludeSegments = Dialog.getNumber();
nbIt = Dialog.getNumber();
showPassChoice = Dialog.getNumber();
if (supressIsolated == 0) showSupressIsolated =1;
testOK=1;
if (excludeObjectsSize <0 || isNaN(excludeObjectsSize)) {
alertMessage = alertMessage + "! Bad settings\: " + "\"Minimum object size\" must be > 0" + ". Replaced by the previous value.\n";
excludeObjectsSize = archexcludeObjectsSize;
testOK=0;
}
if (twigSize <0 || isNaN(twigSize)) {
alertMessage = alertMessage + "! Bad settings\: " + "\"Minimum branch size\" must be \> 0" + ". Replaced by the previous value.\n";
twigSize = archtwigSize;
testOK=0;
}
if (loopSize <0 || isNaN(loopSize)) {
alertMessage = alertMessage + "! Bad settings\: " + "\"Artifactual loop size\" must be \> 0" + ". Replaced by the previous value.\n";
loopSize = archloopSize ;
testOK=0;
}
if (seuilIsolFinal <0 || isNaN(seuilIsolFinal)) {
alertMessage = alertMessage + "! Bad settings\: " + "\"Isolated element size threshold\" must be \> 0" + ". Replaced by the previous value.\n";
seuilIsolFinal = archseuilIsolFinal ;
testOK=0;
}
if (sizeExcludeSegments <0 || isNaN(sizeExcludeSegments)) {
alertMessage = alertMessage + "! Bad settings\: " + "\"Master segment size threshold\" must be \> 0" + ". Replaced by the previous value.\n";
sizeExcludeSegments = archsizeExcludeSegments;
testOK=0;
}
if (nbIt <1 || isNaN(nbIt)) {
alertMessage = alertMessage + "! Bad settings\: " + "\"Iteration number\" must be \>= 1" + ". Replaced by the previous value.\n";
nbIt = archseuilIsolFinal ;
testOK=0;
}
if (showPassChoice > nbIt) showPassChoice = nbIt;
if (showPassChoice < -1 || showPassChoice > nbIt || isNaN(showPassChoice)) {
alertMessage = alertMessage + "! Bad settings\: " + "\"Show iteration\" must be \>= -1 and" + "<= to iteration number, currently =" + nbIt + ". Replaced by the previous value.\n";
showPassChoice = archshowPassChoice ;
testOK=0;
}
}
}
function singleNetworkAnalysis () {
if (is("binary")) exit ("This function requires an 8, 16 or 24 bits image.");
getStatistics(area, mean, min, max, std, histogram);
testDepth=pow(2,bitDepth())-1;
if (bitDepth() == 24) testDepth = 255;
if (mean == 0 || mean == testDepth) exit ("Empty image");
batchChoice=0;
workingImagTemp="";
windowTabName="Stat Results Table"; nameOfStatTab="["+windowTabName+"]";
nameInitImageorFolder="";
starttime=getTime;
imageFolder=getDirectory("image");
findNodes (1);
if (isOpen (workid)) selectImage (workid);
nomdimage = getTitle;
if (lastIndexOf(nomdimage, sufficAn) > 1) {
workingima = substring (nomdimage,0,lastIndexOf(nomdimage, sufficAn));
} else {workingima=nomdimage;}
nameInitImageorFolder=workingima;
if (isOpen (q3id)) selectImage (q3id);
rename(workingima+"-Final Tree (q3)");
if (isOpen (mapExtremaID)) {
selectImage(mapExtremaID);
run("Duplicate...", "title=Map_of_Extremities");
singleAnaMapExtID=getImageID();
selectImage (mapExtremaID); close ();
}
if (isOpen (mapNodesID)) {
selectImage(mapNodesID);
run("Duplicate...", "title=Map_of_Nodes");
singleAnaMapNodeID=getImageID();
selectImage (mapNodesID); close ();
}
if (singleShowMaps == 0) {
if (isOpen (singleAnaMapExtID)) {selectImage (singleAnaMapExtID); close ();}
if (isOpen (singleAnaMapNodeID)) {selectImage (singleAnaMapNodeID); close ();}
if (isOpen (q3id)) {selectImage (q3id); close ();}
if (isOpen(mapMasterTreeID)) {selectImage (mapMasterTreeID); close();}
if (isOpen(masterTreeID)) {selectImage (masterTreeID); close();}
}
seconds = (getTime-starttime)/1000;
setBatchMode("exit and display");
if (isOpen (workid)) selectImage (workid);
menuanalysis=0;
}
function reBuiltMap (couleur) {
currentID=getImageID();
selectImage (rebuiltMapId);
run("Restore Selection");
run("Add Selection...", "stroke=&couleur width=1 ");
run("Select None");
selectImage(currentID);
}
function findTree () {
getStatistics(area, mean, min, max, std, histogram);
testDepth=pow(2,bitDepth())-1;
if (bitDepth() == 24) testDepth = 255;
if (mean == 0 || mean == testDepth) exit ("Empty image");
batchChoice=0;
starttime=getTime;
settings ();
tree ();
if (isOpen (q3id)) {
selectImage (q3id);
run("Invert");
run("Select All");
run("Copy");run("Select None");
} else exit ("No tree found");
if (isOpen (workid)) {
selectImage (workid);
if (bitDepth() == 8 || bitDepth() == 16) run("RGB Color");
run("Duplicate...", "title=tempBlink");
tempBlinkid=getImageID();
setPasteMode("Add");
run("Paste");
run("Select None");
setPasteMode("Copy");
}
seconds = (getTime-starttime)/1000;
selectImage (q3id);
run("Invert");
selectImage (workid);
if (bitDepth() == 8 || bitDepth() == 16) run("RGB Color");
run("Add Image...", "image=tempBlink x=0 y=0 opacity=100");
if (isOpen (tempBlinkid)) {selectImage(tempBlinkid); close();}
selectImage (q3id);
rename(workingima+"-Tree (q3)");
setBatchMode("exit and display");
if (isOpen (workid)) {selectImage(workid);}
rename(workingima+" & Tree (overlay)");
//print ("timing="+seconds +" sec");
}
function FindAnfRemoveLoops () {
if (!is("binary")) exit ("This function requires a binary image.");
getStatistics(area, mean, min, max, std, histogram);
if (mean == 0 || mean == (pow(2,bitDepth())-1)) exit ("Empty image");
batchChoice=0;showLoopInBlue=1;
initLoop=getImageID();
setBatchMode(true);
run("Duplicate...", "title=lookloop");
workid=getImageID();
toAnalyse=getImageID();
archloop=showLoops;
showLoops=1;
findLoop (toAnalyse,0);
nomdimage = getTitle;
showLoops=archloop;showLoopInBlue=0;
selectImage(workid);
if (getInfo("overlay") != "") {
Overlay.copy;
selectImage(initLoop);
Overlay.paste
}
if (isOpen (initLoop)) selectImage (initLoop);
nomdimage = getTitle;
run("Duplicate...", "title=lookloop");
if (lastIndexOf(nomdimage, ".") > 1) {
workingima = substring (nomdimage,0,lastIndexOf(nomdimage, "."));
} else {workingima=nomdimage;}
rename(workingima+"-with Loops");
selectImage (initLoop);
run("Remove Overlay");
if (isOpen (workid)) selectImage (workid);
rename(workingima+"-with Loops Removed (q3)");
run("Select None");
setBatchMode("exit and display");
}
function findExtremities () {
if (!is("binary")) exit ("This function requires a binary image.");
getStatistics(area, mean, min, max, std, histogram);
if (mean == 0 || mean == (pow(2,bitDepth())-1)) exit ("Empty image");
batchChoice=0;
initSkeleton=getImageID();
choix=showOnlyFinal;
showOnlyFinal=0;
nomdimage = getTitle;
initid=getImageID();
imageFolder=getDirectory("image");
sufix= ".";
if (lastIndexOf(nomdimage, sufix) > 1) {
workingima = substring (nomdimage,0,lastIndexOf(nomdimage, sufix));
} else {workingima=nomdimage;}
setBatchMode(true);
run("Make Binary");
selectImage(initSkeleton);
run("Duplicate...", "title=q3Single");
rename(workingima);
workid=getImageID();
run("Duplicate...", "title=q3 bis");
q3id=getImageID();
mapExtrema (q3id,q3id,1,1);
selectImage (q3id);
rename(workingima+"-Extremities (q3)");
showOnlyFinal=choix;
if (isOpen(workid)) {selectImage (workid); close();}
setBatchMode("exit and display");
selectImage (q3id);
}
function findTheNodes () {
if (!is("binary")) exit ("This function requires a binary image.");
getStatistics(area, mean, min, max, std, histogram);
if (mean == 0 || mean == (pow(2,bitDepth())-1)) exit ("Empty image");
batchChoice=0;
initSkeleton=getImageID();
choix=showOnlyFinal;
showOnlyFinal=0;
nomdimage = getTitle;
initid=getImageID();
imageFolder=getDirectory("image");
sufix= ".";
if (lastIndexOf(nomdimage, sufix) > 1) {
workingima = substring (nomdimage,0,lastIndexOf(nomdimage, sufix));
} else {workingima=nomdimage;}
setBatchMode(true);
run("Make Binary");
selectImage(initSkeleton);
run("Duplicate...", "title=q3Single");
rename(workingima);
workid=getImageID();
run("Duplicate...", "title=q3 bis");
q3id=getImageID();
mapNodes (q3id,q3id,1,1,"Nodes");
selectImage (q3id);
rename(workingima+"-Nodes (q3)");
showOnlyFinal=choix;
if (isOpen(workid)) {selectImage (workid); close();}
setBatchMode("exit and display");
selectImage (q3id);
}
function findNodesAndBranches () {
if (!is("binary")) exit ("This function requires a binary image.");
getStatistics(area, mean, min, max, std, histogram);
if (mean == 0 || mean == (pow(2,bitDepth())-1)) exit ("Empty image");
batchChoice=0;
mapExtremaID=0;mapNodesID=0;mapJunctionID=0; mapSegmentID=0; mapBranchID=0; mapMasterTreeID; masterTreeID; mapSegment2Id=0;
initSkeleton=getImageID();
choix=showOnlyFinal;
showOnlyFinal=0;
nomdimage = getTitle;
initid=getImageID();
imageFolder=getDirectory("image");
sufix= ".";
if (lastIndexOf(nomdimage, sufix) > 1) {
workingima = substring (nomdimage,0,lastIndexOf(nomdimage, sufix));
} else {workingima=nomdimage;}
setBatchMode(true);
run("Make Binary");
selectImage(initSkeleton);
run("Duplicate...", "title=q3Single");
rename(workingima);
workid=getImageID();
run("Duplicate...", "title=q3 bis");
q3id=getImageID();
simpleNode ();
selectImage (workid);
rename(workingima+"-Twig Map");
selectImage (q3id);
rename(workingima+"-Nodes & Extremities (q3)");
showOnlyFinal=choix;
}
function analyseFromATree () {
if (!is("binary")) exit ("This function requires a binary image.");
getStatistics(area, mean, min, max, std, histogram);
if (mean == 0 || mean == (pow(2,bitDepth())-1)) exit ("Empty image");
batchChoice=0;
workingImagTemp="";
windowTabName="Stat Results Table"; nameOfStatTab="["+windowTabName+"]";
nameInitImageorFolder="";
initSkeletonID=getImageID();
mapExtremaID=0;mapNodesID=0;mapJunctionID=0; mapSegmentID=0; mapBranchID=0; mapMasterTreeID; masterTreeID; mapSegment2Id=0;
nomdimage = getTitle;
workingima=nomdimage;
nameInitImageorFolder=workingima;
initid=getImageID();
imageFolder=getDirectory("image");
imageFolderSave=imageFolder;
sufix= ".";
if (lastIndexOf(nomdimage, sufix) > 1) {
workingima = substring (nomdimage,0,lastIndexOf(nomdimage, sufix));
} else {workingima=nomdimage;}
run("Select None");
titre=workingima+sufficAn;
workingima=workingima+sufficAn;
setBatchMode(true);
run("Make Binary");
selectImage(initSkeletonID);
run("Duplicate...", "title=q3Single");
workid=getImageID();
rename(workingima);
run("Duplicate...", "title=q3 bis");
q3id=getImageID();
starttime=getTime;
findNodes (0);
imageFolder=imageFolderSave;
if (isOpen (mapExtremaID)) {
selectImage(mapExtremaID);
run("Duplicate...", "title=Map_of_Extremities");
singleAnaMapExtID=getImageID();
selectImage (mapExtremaID); close ();
}
if (isOpen (mapNodesID)) {
selectImage(mapNodesID);
run("Duplicate...", "title=Map_of_Nodes");
singleAnaMapNodeID=getImageID();
selectImage (mapNodesID); close ();
}
if (isOpen (initSkeletonID)) {
selectImage (initSkeletonID);
close ();
}
if (isOpen (q3id)) {
selectImage (q3id);
rename(workingima);
}
if (singleShowMaps == 0) {
if (isOpen (singleAnaMapExtID)) {selectImage (singleAnaMapExtID); close ();}
if (isOpen (singleAnaMapNodeID)) {selectImage (singleAnaMapNodeID); close ();}
if (isOpen(mapMasterTreeID)) {selectImage (mapMasterTreeID); close();}
if (isOpen(masterTreeID)) {selectImage (masterTreeID); close();}
}
seconds = (getTime-starttime)/1000;
setBatchMode("exit and display");
if (isOpen (workid)) selectImage (workid);
menuanalysis=0;
}
function getMapsOFSelections () {
setBatchMode(true);
var segmentCount=0, branchCount=0, extremityCount=0, extremityCountEdge=0, junctionCount=0, twigCount=0, nodeCount=0, masterJunctionCount=0, masterSegmentCount=0;
var isolatedElementCount=0, meshCount=0, isolatedTwigCount=0;
run("Duplicate...", "title=tempOverlay");
tempOverlayID = getImageID();
run("To ROI Manager");
getDimensions(width, height, channels, slices, frames);
newImage("Re-Built Map", "8-bit White", width, height, 1);
rebuiltMapId = getImageID();
Array.fill(reBuiltChoicesNames,0);
if(roiManager("count")<= 0) exit ("nothing in the ROI Manager");
nbselections=roiManager("count");
Dialog.create("Re-Built Map Choices");
Dialog.addMessage("Choose the elements of the map");
for (i=0; i< lengthOf(reBuiltElements); i++) {
Dialog.addCheckbox(reBuiltElements[i], reBuiltChoices [i]) ;
}
Dialog.show();
for (i=0; i< lengthOf(reBuiltElements); i++) {
reBuiltChoices [i] = Dialog.getCheckbox();
if (reBuiltChoices [i] == 1) reBuiltChoicesNames [i] = reBuiltElements[i];
}
selectImage (tempOverlayID);
for (i=0; i< nbselections; i++) {
roiManager("select",i);
colorSelection = getInfo("selection.color");
cathegory="";
if (toString(colorSelection) == toString(extremityCoul)) {extremityCount++; cathegory="extremity"; name="extremity-"+extremityCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(extremityEdgeCoul)) {extremityCountEdge++; cathegory="extremityEdge"; name="extremityEdge-"+extremityCountEdge; roiManager("Rename",name);}
if (toString(colorSelection) == toString(junctionCoul)) {junctionCount++; cathegory="junction"; name="junction-"+junctionCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(twigColour)) {twigCount++; cathegory="twig";name="twig-"+twigCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(segmentCoul)) {segmentCount++; cathegory="segment";name="segment-"+segmentCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(branchCoul)) {branchCount++; cathegory="branch";name="branch-"+branchCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(nodesCoul)) {nodeCount++; cathegory="nodes";name="nodes-"+nodeCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(masterJunctionCoul)) {masterJunctionCount++; cathegory="masterJunction";name="masterJunction-"+masterJunctionCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(masterSegmentCoul)) {masterSegmentCount++; cathegory="masterSegment";name="masterSegment-"+masterSegmentCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(isolatedElementCoul)) {isolatedElementCount++; cathegory="isolatedElement";name="isolatedElement-"+isolatedElementCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(meshCoul)) {meshCount++;cathegory="mesh"; name="mesh-"+meshCount; roiManager("Rename",name);}
if (toString(colorSelection) == toString(isolatedTwigCoul)) {isolatedTwigCount++; cathegory="isolatedTwig";name="isolatedTwig-"+isolatedTwigCount; roiManager("Rename",name);}
for (j=0; j< lengthOf(reBuiltElements); j++) {
if (cathegory == reBuiltChoicesNames[j]) { reBuiltMap (colorSelection); }
}
name = "";
}
if (isOpen (tempOverlayID)) {selectImage (tempOverlayID); close();}
setBatchMode("exit and display");
}
function findNodes (treeOption) {
if (batchChoice == 0 && (treeOption == 1) && (menuanalysis==0)) settings ();
meanBgGreenValue=0;
workid=getImageID();
getStatistics(area, mean, min, max, std, histogram);
testDepth=pow(2,bitDepth())-1;
if (bitDepth() == 24) testDepth = 255;
if (mean != 0 && mean != testDepth) {
//step=0;
if (treeOption == 1) tree ();
run("Options...", "iterations=1 count=1 edm=Overwrite do=Nothing");
node ();
selectImage (workid);
metaResults="Results for vascular branching analysis:\n";
metaResults=metaResults+ "Analyzed area="+analyzedArea+ " timing=" +seconds +" sec\n";
metaResults=metaResults+"nb Extrema="+ nbExtrema +" nb Nodes="+ nbNodes + " nb Junctions=" + nbJunctions + "\n";
metaResults=metaResults+"Nb master segments="+ nbMasterSgment + " Tot. master segments lenght="+ totalMasterSegmentLenght + "\n";
metaResults=metaResults+"Nb meshes="+ nbMesh + " Tot.meshes area="+ totalMeshSize + "\n";
metaResults=metaResults+"nb total peaces="+ nbTotalPeaces +" nb segments="+ nbSegments + " nb branches="+ nbTwigs + " nb isolated segments="+ nbIsolated+"\n";
metaResults=metaResults+"Total lenght="+totalLenght+ " total branching lenght="+totalBranchingLenght +"\n";
metaResults=metaResults+"Total segments lenght="+totalSegmentsLenght+" total branches lenght="+ totalTwigsLenght + " total isolated branches lenght="+totalIsolatedLenght+"\n";
metaResults=metaResults+"Branching interval=" + branchingIndex + " Mesh Index=" + meshIndex + " Mean Mesh Size = " + meanMeshSize + "\n";
metaResults=metaResults+"Path of analyzed file=" + imageFolder ;
selectImage (workid);
setMetadata("Info", metaResults);
} else {
workingima=getTitle();
if (lastIndexOf(workingima, ".") > 1) {
workingima = substring (workingima,0,lastIndexOf(workingima, "."));
}
rename (workingima);
run("Clear Results");
analyzedArea=0; nbExtrema=0; nbNodes=0; nbJunctions=0; nbMasterJunctionsFinal=0; nbMasterSgment=0; totalMasterSegmentLenght=0; nbMesh=0; totalMeshSize=0; nbTotalPeaces=0; nbSegments=0; nbTwigs=0; nbIsolated=0; totalLenght=0; totalBranchingLenght=0; totalSegmentsLenght=0; totalTwigsLenght=0; totalIsolatedLenght=0; branchingIndex=0; meshIndex=0; meanMeshSize=0;
}
if (recordStepOption == 1) {
workingimaArch=workingima;
workingima = workingima + "-step=" + step;
TabWindow (1);
workingima = workingimaArch;
titreStep=" pass="+stepByStep+"-step"+ (step++);
recordSteps (workid,workingima,titreStep);
} else {
TabWindow (1);
}
return workid;
}
function tree () {
requires("1.43f");
setBatchMode(true);
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
depth = bitDepth; nbslice = getSliceNumber();
if (depth != 24 && (objects == 1)) exit('Image must be 8 bit RGB encoded');
if (bitDepth() == 24 && objects == 2) exit('Image must be 8 or 16 bits encoded');
nomdimage = getTitle;
initid=getImageID();
imageFolder=getDirectory("image");
sufix= ".";
if (lastIndexOf(nomdimage, sufix) > 1) {
workingima = substring (nomdimage,0,lastIndexOf(nomdimage, sufix));
} else {workingima=nomdimage;}
run("Select None");
titre=workingima+sufficAn;
workingima=workingima+sufficAn;
run("Duplicate...", "title=&titre");
workid = getImageID();
if (objects == 1) q3id = treeHUVECPhase(workid); // HUVEC Phase contrast
if (objects == 2) q3id = treeHUVECFluo(workid); // HUVEC fluo
selectImage (q3id);
setForegroundColor (255,255 ,255);
getDimensions(width, height, channels, slices, frames);
setLineWidth(1);drawRect(0, 0, width, height);
run("Options...", "iterations=1 count=1 edm=Overwrite do=Nothing");
}
function treeHUVECPhase(workid) {
run("Duplicate...", "title=initRGB");
imaid=getImageID();
if (rmspeckles==1) {
// find small bright objects
selectImage (imaid);
run("RGB Stack");
setSlice(2);
run("Duplicate...", "temp");
tempIDee=getImageID();
selectImage (imaid);
run("RGB Color");
selectImage (tempIDee);
deflouageRelief2(tempIDee);
histoAnalyse(1,"Mean");
segmentSpec ();
specID=getImageID();
selectImage (tempIDee); close ();
selectImage (specID);rename ("speckles");
run("Dilate");
}
selectImage (imaid);
run("RGB Stack");
setSlice(2);
run("Duplicate...", "tempfinale");
run("Select All");
run("Copy"); close ();
selectImage (imaid);
run("RGB Color");
run("8-bit");
run("Paste");
run("Select None");
deflouageRelief(imaid);
run("Maximum...", "radius=0");
run("Gaussian Blur...", "sigma=0.1");
histoAnalyse(1,"MinError");
if (rmspeckles==1) {
imageCalculator("Subtract ", imaid,specID);
if (isOpen (specID)) {selectImage (specID); close ();}
selectImage (imaid);
}
segMaskMeas=getTitle(); segMaskMeasid=getImageID();
rename("q3"); q3Name=getTitle;
q3id = getImageID();
run("Options...", "iterations=2 count=3 pad edm=Overwrite do=Erode");
run("Skeletonize");
run("Options...", "iterations=2 count=2 pad edm=Overwrite do=Dilate");
run("Skeletonize");
selectImage(q3id);
return q3id;
}
function deflouageRelief(tempDEid) {
selectImage(tempDEid);
run("Bandpass Filter...", "filter_large=10 filter_small=0 suppress=None tolerance=5 autoscale");
run("Duplicate...", "title=tempdefloue");
tempdefloueID=getImageID();
run("Enhance Contrast", "saturated=0 normalize ");
selectImage(tempDEid);
run("Enhance Contrast", "saturated=0 normalize "); // a verifier
run("Find Edges");
imageCalculator("Average", tempDEid,tempdefloueID);
selectImage(tempdefloueID); close ();
selectImage (tempDEid);
}
function deflouageRelief2(tempDEid) {
selectImage(tempDEid);
run("Bandpass Filter...", "filter_large=10 filter_small=0 suppress=None tolerance=5 autoscale");
run("Find Edges");
}
function treeHUVECFluo (workid) {
selectImage(workid);
run("Duplicate...", "title=initRGB");
setAutoThreshold("Percentile dark");
run("Convert to Mask");
run("Options...", "iterations=1 count=1 pad edm=Overwrite");
run("Dilate");
run("Skeletonize");
rename("q3"); q3Name=getTitle;
q3id = getImageID();
return q3id;
}
function segmentSpec () {
//Speckelradius=2;
limiteSpec=floor((Speckelradius*Speckelradius)*3);
run("Set Measurements...", "area min perimeter shape redirect=None decimal=2");
run("Analyze Particles...", "size=2-"+(limiteSpec)+" circularity=0-1.00 show=Masks clear");
}
function findLoop (treeID,showBigLoops) {
if (! is("Batch Mode")) {setBatchMode(true);}
nbLoop=1;
nbMesh=0; totalMeshSize=0;
if (isOpen (treeID)) selectImage (treeID); else exit ("no tree image available");
nom="loopTemp";
run("Duplicate...", "title=&nom");
loopTempID = getImageID();
run("Options...", "iterations=1 count=1 edm=Overwrite do=Dilate");
nom="q3-loops";
run("Duplicate...", "title=&nom");
loopsID = getImageID();
getDimensions(width, height, channels, slices, frames);
selectImage (loopTempID);
getStatistics(area, mean, min, max, std, histogram);
loopTemp=histogram[255];
while (loopTemp != 0) {
nbLoop=0;
setThreshold(255, 255, "none");
run("Set Measurements...", "area min perimeter redirect=None decimal=2");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing clear include record");
for (i=0; i< nResults; i++) {
selectImage (loopTempID);
setThreshold(255, 255, "red");
doWand(getResult("XStart",i), getResult("YStart",i),0, "8-connected");
getStatistics(area, mean, min, max, std, histogram);
// erease objects without loop
if (histogram[0] == 0) {
selectImage (loopTempID);
run("Clear", "slice");
run("Select None");
}
// invert object containing almost on level of loop
if (histogram[0] != 0) {
run("Invert");run("Select None");
nbLoop ++;
}
}
run("Select None");
// remove loops from loopTemp, add loops in q3-loops - loops containing onbject kept in loopTemp
if (nbLoop > 0) {
selectImage (loopTempID);
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing clear include record");
selectImage (loopTempID);
if (nResults > 0) {
for (i=0; i< nResults; i++) {
selectImage (loopTempID);
doWand(getResult("XStart",i), getResult("YStart",i),0, "8-connected");
getStatistics(area, mean, min, max, std, histogram);
if (histogram[0] == 0) {
run("Clear", "slice");run("Select None");
if (area < loopSize) {
selectImage (loopsID);
run("Restore Selection");
run("Invert");
run("Select None");
if (showLoops == 1 && isOpen(workid)) {
selectImage (workid);
run("Restore Selection");
run("Enlarge...", "enlarge=1");
if (showLoopInBlue==1) {
run("Add Selection...", "stroke=blue width=1 ");
} else {
run("Add Selection...", "stroke=yellow width=1 ");
}
run("Select None");
}
} else {
if (showBigLoops == 1) {
// detect meshes
selectImage (workid);
run("Restore Selection");
nbMesh ++;
getStatistics(area, mean, min, max, std, histogram);
totalMeshSize = totalMeshSize + area;
run("Enlarge...", "enlarge=-8");
run("Add Selection...", "stroke=&meshCoul width=2 ");
run("Select None");
}
}
} else {
run("Invert");run("Select None");
if (showBigLoops == 1) {
// detect meshe included in another meshe
selectImage (workid);
run("Restore Selection");
nbMesh ++;
getStatistics(area, mean, min, max, std, histogram);
totalMeshSize = totalMeshSize + area;
run("Enlarge...", "enlarge=-8");
run("Add Selection...", "stroke=&meshCoul width=2 ");
run("Select None");
}
}
}
}
}
selectImage (loopTempID);
getStatistics(area, mean, min, max, std, histogram);
loopTemp=histogram[255];
} // end while
run("Select None");
selectImage (loopTempID);
getStatistics(area, mean, min, max, std, histogram);
loopTemp=histogram[255];
if (isOpen (loopTempID)) {selectImage (loopTempID); close ();}
if (isOpen (loopsID)) {
selectImage (loopsID);
run("Skeletonize");
run("Select All");
run("Copy"); close();
selectImage (treeID);
setPasteMode("Copy");
run("Paste");
}
if (totalMeshSize >0 && nbMesh > 0) {meanMeshSize=d2s((totalMeshSize/nbMesh),1);} else {meanMeshSize=0;}
setForegroundColor (255,255 ,255);
getDimensions(width, height, channels, slices, frames);
setLineWidth(1);drawRect(0, 0, width, height);
}
//setBatchMode("exit and display");
//exit
function simpleNode () {
// note: q3id contains the tree
if (isOpen (q3id)) selectImage (q3id); else exit ("no tree image available");
getStatistics(area, mean, min, max, std, histogram);
analyzedArea=area;
totalLenght=0; totalSegmentsLenght=0; totalTwigsLenght=0; totalBranchingLenght=0; branchingIndex=0; meshIndex=0;
mapExtremaID= mapExtrema (q3id,workid,1,0);
mapNodesID= mapNodes (q3id,workid,1,0,"Nodes");
mapTwigID=twigMap (q3id,workid,mapExtremaID,mapNodesID,0);
mapExtremaID= mapExtrema (q3id,q3id,1,0);
mapNodesID= mapNodes (q3id,q3id,1,0,"Nodes");
if (isOpen (mapTwigID)) {selectImage (mapTwigID); close ();}
if (isOpen (mapExtremaID)) {selectImage (mapExtremaID); close ();}
if (isOpen (mapNodesID)) {selectImage (mapNodesID); close ();}
if (isOpen (mapJunctionID)) {selectImage (mapJunctionID); close ();}
if (isOpen (mapSegmentID)) {selectImage (mapSegmentID); close ();}
if (isOpen (mapBranchID)) {selectImage (mapBranchID); close ();}
}
function node () {
// note: q3id contains the tree
if (isOpen (q3id)) selectImage (q3id); else exit ("no tree image available");
getStatistics(area, mean, min, max, std, histogram);
analyzedArea=area;
totalLenght=0; totalSegmentsLenght=0; totalTwigsLenght=0; totalBranchingLenght=0; branchingIndex=0; meshIndex=0;
pass = -1; // initial branching
if (showPassChoice <0) {
mapExtremaID= mapExtrema (q3id,workid,1,0);
mapNodesID= mapNodes (q3id,workid,1,0,"Nodes");
}
if (showPassChoice >=0) {
mapExtremaID= mapExtrema (q3id,workid,0,0);
mapNodesID= mapNodes (q3id,workid,0,0,"Nodes");
}
for (pass=0; pass<= nbIt; pass++) {
if (showPassChoice >= pass) {
if (pass <2 && findloopOption == 1) {
findLoop (q3id,0); // remove loops created by the first main simplification
mapExtremaID= mapExtrema (q3id,workid,0,0);
mapNodesID= mapNodes (q3id,workid,0,0,"Nodes");
}
cutTwig=1;
if (pass==showPassChoice) cutTwig=0;
mapTwigID=twigMap (q3id,workid,mapExtremaID,mapNodesID,cutTwig);
if (isOpen (mapTwigID)) {selectImage (mapTwigID); close ();}
if (isOpen (mapExtremaID)) {selectImage (mapExtremaID); close ();}
if (isOpen (mapNodesID)) {selectImage (mapNodesID); close ();}
if (isOpen (q3id) && smoothEachLimbing ==1) {
// to smooth the zig-zag aspect after limbing and to avoid edge effects
selectImage (q3id);
run("Smooth");
run("Maximum...", "radius=3");
run("Make Binary");
run("Skeletonize");
setForegroundColor (255,255 ,255);
getDimensions(width, height, channels, slices, frames);
setLineWidth(8);drawRect(0, 0, width, height);
setLineWidth(1);
setThreshold(255, 255, "none");
}
//mapExtremaID= mapExtrema (q3id,workid,1,0);
mapExtremaID= mapExtrema (q3id,workid,1,1);
mapNodesID= mapNodes (q3id,workid,1,1,"Nodes");
if (pass==showPassChoice && showMesh==1 && analyseMasterTree==0) {
findLoop (q3id,1);
}
if (isOpen (mapJunctionID)) {selectImage (mapJunctionID); close ();}
if (isOpen (mapSegmentID)) {selectImage (mapSegmentID); close ();}
if (isOpen (mapBranchID)) {selectImage (mapBranchID); close ();}
}
}
}
function twigMap (q3twigid,destination,extremeID,nodesID,rmTwigy) {
if (mapSegmentID ==1) {selectImage (mapSegmentID); close();}
if ( !isOpen (extremeID) || !isOpen (nodesID) || !isOpen (q3twigid)) exit ("No maps available");
getDimensions(width, height, channels, slices, frames);
newImage("map Segments", "8-bit White", width, height, 1);
mapSegmentID = getImageID();
if (isOpen(mapBranchID)) {selectImage(mapBranchID); close();}
getDimensions(width, height, channels, slices, frames);
newImage("map Twigs", "8-bit White", width, height, 1);
mapBranchID = getImageID();
// to remove small segments
if (isOpen (nodesID) && supressVerySmallSegments == 1) {
// to avoide too small segments betxeen two near nodes
selectImage (nodesID);
nom="finalmapBigNodes";
run("Duplicate...", "title=&nom");
run("Options...", "iterations=1 count=1 edm=Overwrite do=Dilate");
finalmapBigNodesID= getImageID();
imageCalculator("Subtract create", q3twigid,finalmapBigNodesID);
mapTwigID= getImageID(); // contains segments separated by nodes
} else {
imageCalculator("Subtract create", q3twigid,nodesID);
mapTwigID= getImageID(); // contains segments separated by nodes
}
selectImage (mapTwigID);
rename ("twigDetection and Analysis");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing clear include record");
nbSegments=0;nbTwigs=0;nbIsolated=0;nbTotalPeaces=0;
totalLenght=0; totalTwigsLenght=0; totalSegmentsLenght=0; totalBranchingLenght=0; totalIsolatedLenght=0;
segmentcount=0;
if (nResults > 0) {
for (i=0; i< nResults; i++) {
selectImage (mapTwigID);
longueurSegment= floor (getResult ("Perim.",i)/2);
doWand(getResult("XStart",i), getResult("YStart",i),0, "8-connected");
xstartSelect=getResult("XStart",i);
ystartSelect=getResult("YStart",i);
selectImage (extremeID);
run("Restore Selection");
getStatistics(area, mean, min, max, std, histogram);
extremHisto=histogram;
rmCol=0;supress=0;
if (extremHisto [255] ==1 ) {
if (area < twigSize) {
supress=1;
showSelection=0;
if (showOnlyFinal == 1 && pass == showPassChoice && showTwig==1) showSelection=1;
if (showOnlyFinal == 0 && showTwig==1) showSelection=1;
if (showSelection == 1 && isOpen (destination) && rmCol==0) {
selectImage (destination);
run("Restore Selection");
run("Add Selection...", "stroke=&twigColour width=1"); // show too short twigs as overlay
selectImage (mapBranchID);
run("Restore Selection");
run("Add Selection...", "stroke=&twigColour width=1"); // show too short twigs as overlay
setForegroundColor(0, 0, 0);
run("Fill", "slice");
run("Select None");
nbTwigs++; totalTwigsLenght=totalTwigsLenght+longueurSegment;
}
} else {
if (rmCol==0) {
nbTwigs++; totalTwigsLenght=totalTwigsLenght+longueurSegment;
// place to put the mean green value of twig for futur option of color sorting
}
run("Select None");
showSelection=0;
if (showOnlyFinal == 1 && pass == showPassChoice && showTwig==1) showSelection=1;
if (showOnlyFinal == 0 && showTwig==1) showSelection=1;
if (showSelection == 1 && isOpen (destination) && rmCol==0) {
// futur color test here
selectImage (destination);
run("Restore Selection");
run("Add Selection...", "stroke=&branchCoul width=1"); // show twigs as overlay
selectImage (mapBranchID);
run("Restore Selection");
run("Add Selection...", "stroke=&branchCoul width=1"); // show nodes as overlay
setForegroundColor(0, 0, 0);
run("Fill", "slice");
run("Select None");
}
}
if (supress == 1 && supressTwig ==1 && rmTwigy && rmCol==0) {
selectImage (mapTwigID);
run("Restore Selection");
run("Clear", "slice");
run("Select None");
}
}
if (extremHisto [255] == 2 ) {
if (supressIsolated == 0 && rmCol==0 && longueurSegment > seuilIsolFinal) {totalIsolatedLenght=totalIsolatedLenght+longueurSegment; nbIsolated ++;}
showSelection=0;
if (showOnlyFinal == 1 && pass == showPassChoice && showTwig==1) showSelection=1;
if (showOnlyFinal == 0 && showTwig==1) showSelection=1;
if (showSelection == 1 && isOpen (destination) && rmCol==0) {
selectImage (destination);
run("Restore Selection");
if (supressIsolated == 0 && longueurSegment > seuilIsolFinal) {run("Add Selection...", "stroke=&isolatedElementCoul width=1");}
if (supressIsolated == 1 && showSupressIsolated == 1) {run("Add Selection...", "stroke=&isolatedTwigCoul width=1"); }
if (showSupressIsolated == 1 && longueurSegment <= seuilIsolFinal) {run("Add Selection...", "stroke=&isolatedTwigCoul width=1");}
run("Select None");
if (supressIsolated == 1 || longueurSegment < seuilIsolFinal && rmCol==0) {
selectImage (mapTwigID);
run("Restore Selection");
run("Clear", "slice");
run("Select None");
}
}
}
if (extremHisto [255] == 0) {
if (rmCol==0) {nbSegments ++; totalSegmentsLenght=totalSegmentsLenght+longueurSegment;}
showSelection=0;
if (showOnlyFinal == 1 && pass == showPassChoice && showSegments==1) showSelection=1;
if (showOnlyFinal == 0 && showTwig==1) showSelection=1;
if (showSelection == 1 && isOpen (destination) && rmCol==0) {
// futur test for color here
selectImage (destination);
run("Restore Selection");
run("Add Selection...", "stroke=&segmentCoul width=1"); // show segment as overlay
selectImage (mapSegmentID);
run("Restore Selection");
setForegroundColor(0, 0, 0);
run("Fill", "slice");
run("Add Selection...", "stroke=&segmentCoul width=1"); // show segment as overlay
run("Select None");
selectImage (mapSegmentID);
run("Select None");
}
}
}
selectImage (mapTwigID);
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing clear include record");
}
run("Select None");
if (supressVerySmallSegments == 0) imageCalculator("Add ", mapTwigID, nodesID);
if (isOpen (nodesID) && isOpen (finalmapBigNodesID) && supressVerySmallSegments == 1 ) {
if (isOpen(finalmapBigNodesID)) {
selectImage (finalmapBigNodesID);
getStatistics(area, mean, min, max, std, histogram);
}
if (isOpen(finalmapBigNodesID) && max!=0) {
selectImage (finalmapBigNodesID);
run("Options...", "iterations=1 count=1 edm=Overwrite do=Dilate");
imageCalculator("Add ", mapTwigID, finalmapBigNodesID);
selectImage (mapTwigID);
}
}
selectImage (mapTwigID);
run("Select None");
rename ("twig resolve");
run("Skeletonize");
// remove smal objects
setForegroundColor (255,255 ,255);
getDimensions(width, height, channels, slices, frames);
setLineWidth(1);drawRect(0, 0, width, height);
setThreshold(255, 255, "none");
run("Analyze Particles...", "size=["+(excludeObjectsSize)+"] -Infinity circularity=0.00-1.00 show=Masks clear record");
masqueid=getImageID();
if (nResults >0) {
rename ("mask"+pass);
run("Select All");
run("Copy");
selectImage (mapTwigID);
setPasteMode("Copy");
run("Paste");
run("Select None");
}
selectImage (masqueid); close ();
selectImage (mapTwigID);
run("Select All");
run("Copy");
selectImage (q3twigid);
run("Paste");
run("Select None");
if (isOpen(finalmapBigNodesID)) {
selectImage (finalmapBigNodesID);
getStatistics(area, mean, min, max, std, histogram);
if (max ==0) close ();
}
// option analyseMasterTree
if (analyseMasterTree == 1 && (nbSegments >1) && pass == showPassChoice) {
masterJunstionMap (mapSegmentID, destination);
}
if (isOpen(finalmapBigNodesID)) {selectImage(finalmapBigNodesID); close ();}
if (isOpen (smootMapID)) {selectImage (smootMapID); close ();}
// end option analyseMasterTree
selectImage (q3twigid);
run("Select None");
selectImage (mapTwigID);
run("Select None");
nbTotalPeaces= nbIsolated+nbTwigs+nbSegments;
totalTwigsLenght=floor(totalTwigsLenght);
totalIsolatedLenght=floor(totalIsolatedLenght);
totalSegmentsLenght=floor(totalSegmentsLenght);
totalBranchingLenght=totalSegmentsLenght+totalTwigsLenght;
totalLenght=totalBranchingLenght+totalIsolatedLenght;
if (totalSegmentsLenght >=1 && nbTwigs >0) { branchingIndex=d2s((totalSegmentsLenght/(nbTwigs)),3);} else {branchingIndex =0;}
return mapTwigID;
}
function masterJunstionMap (mapSegment2Id, destination2ID) {
setForegroundColor (255, 255, 255);
nbMasterSgment=0; totalMasterSegmentLenght=0;
nom="masterTreeID";
if (isOpen(finalmapBigNodesID) && supressVerySmallSegments == 1) {
// method without the very small segments
selectImage (mapSegment2Id);
run("Invert");
imageCalculator("Add create", mapSegment2Id,finalmapBigNodesID); // verifier si n�c�ssaire
setThreshold(255, 255, "none");
rename(nom);
masterTreeID=getImageID();
run("Invert");
run("Skeletonize");
run("Invert");
mapNodes (masterTreeID,destination2ID,1,0,"MasterNodes");
} else {
// method with the very small segments
selectImage(nodesID);
run("Select None");
nom2="tempSmoothNodesMap";
run("Duplicate...", "title=&nom2");
smootMapID = getImageID();
run("Options...", "iterations=1 count=3 edm=Overwrite do=Dilate");
selectImage (mapSegment2Id);
run("Invert");
imageCalculator("Add create", mapSegment2Id,smootMapID);
rename(nom);
masterTreeID=getImageID();
run("Invert");
run("Skeletonize");
run("Invert");
mapNodes (masterTreeID,destination2ID,1,0,"MasterNodes");
}
// calulates and overlay the master segments
imageCalculator("Multiply create", mapMasterJunctionID,masterTreeID);
rename ("mapMasterTree");
mapMasterTreeID = getImageID();
run("Invert");
getDimensions(width, height, channels, slices, frames);
setForegroundColor (255, 255, 255);
setLineWidth(1);drawRect(0, 0, width, height);
setForegroundColor (0, 0, 0);
run("Select None");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing clear include record");
// quantify and plot master segments
nbMasterSgment = nResults;
if (nResults > 0) {
for (i=0; i< nResults; i++) {
selectImage (mapMasterTreeID);
longueurSegment= floor (getResult ("Perim.",i)/2);
doWand(getResult("XStart",i), getResult("YStart",i),0, "8-connected");
getStatistics(area, mean, min, max, std, histogram);
if (min != max) longueurSegment= floor (getResult ("Perim.",i));
if (min == max) longueurSegment= floor (getResult ("Perim.",i)/2);
// option to supress small master segments
ereaseSegment=0;
if (longueurSegment <= sizeExcludeSegments && supressSmallSegments ==1) {
ereaseSegment=1;
}
xstartSelect=getResult("XStart",i);
ystartSelect=getResult("YStart",i);
if (ereaseSegment==0) {
selectImage (mapSegment2Id);
run("Restore Selection");
if (showMasterSegments==1) run("Add Selection...", "stroke=&masterSegmentCoul width=2");
run("Select None");
selectImage (destination2ID);
run("Restore Selection");
if (showMasterSegments==1) run("Add Selection...", "stroke=&masterSegmentCoul width=2");
run("Select None");
selectImage (mapMasterTreeID);
run("Select None");
totalMasterSegmentLenght = totalMasterSegmentLenght + longueurSegment;
} else {
selectImage (mapSegment2Id);
run("Restore Selection");
run("Clear", "slice");
run("Select None");
selectImage (mapMasterJunctionID);
run("Restore Selection");
run("Enlarge...", "enlarge=2");
run("Fill", "slice");
run("Select None");
nbMasterSgment=nbMasterSgment-1;
}
}
}
// plot the master junction (and quantify the merged nodes)
selectImage (mapMasterJunctionID);
run("Select None");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing clear include record");
if (nResults > 0) {
nbMasterJunctions=0;
for (i=0; i< nResults; i++) {
selectImage (mapMasterJunctionID);
doWand(getResult("XStart",i), getResult("YStart",i),0, "8-connected");
run("Select None");
selectImage (destination);
run("Restore Selection");
run("Enlarge...", "enlarge=4");
run("Add Selection...", "stroke=&masterJunctionCoul width=2 "); // show master junction as overlay
run("Select None");
nbMasterJunctions ++;
}
}
if (showMesh==1 && analyseMasterTree==1) {
selectImage (masterTreeID);
run("Invert LUT");
findLoop (masterTreeID,1);
}
nbMasterJunctionsFinal=nbMasterJunctions;
if (totalMasterSegmentLenght > 0 && nbMasterJunctions > 0) meshIndex=d2s((totalMasterSegmentLenght/(nbMasterJunctions)),3); else {
meshIndex =0;}
}
// return the mean value of an histogram
function MeanStatHisto (histo,mini,maxi) {
volhisto=0;meanhisto=0;nbPixel=0;
if ((maxi-mini) > 0 ) {
for (i=mini; i<= maxi; i++) {
volhisto=volhisto +(i* histo[i]);
nbPixel=nbPixel+(histo[i]);
}
}
if (nbPixel >0) meanhisto=volhisto/nbPixel;
return meanhisto;
}
function mapExtrema (binID,destination,overlay,keepPreviousMap) {
//return mapExtremaID which contains the limits (as 1x1 pixels dots)
nbExtrema=0;
if (isOpen(mapExtremaID) && keepPreviousMap==0) {selectImage (mapExtremaID); close();} //else {exit ("no tree image available");}
if (isOpen (binID)) {selectImage (binID);} else {exit ("no tree image available");}
nomdArbre=getTitle;
nom="mapExtrema";
run("Duplicate...", "title=&nom");
mapExtremaID = getImageID();
roiManager("Show None");
run("Remove Overlay");
selectImage (mapExtremaID);
getDimensions(width, height, channels, slices, frames);
setBackgroundColor (255, 255, 255);
setForegroundColor (0, 0, 0);
run("Select All");
run("Clear", "slice");run("Select None");
showSelection=0;
if (showOnlyFinal == 1 && pass == showPassChoice && overlay==1) showSelection=1;
if (showOnlyFinal == 0 && showExtrema==1 && overlay==1) showSelection=1;
for (j=0; j<height; j++) {
for (i=0; i<width; i++) {
selectImage(binID);
environs=0;
snif = getPixel(i,j);
if (snif > 0) {
if (getPixel(i-1,j-1) == 255) environs ++;
if (getPixel(i,j-1) == 255) environs ++;
if (getPixel(i+1,j-1) == 255) environs ++;
if (getPixel(i-1,j) == 255) environs ++;
if (getPixel(i+1,j) == 255) environs ++;
if (getPixel(i-1,j+1) == 255) environs ++;
if (getPixel(i,j+1) == 255) environs ++;
if (getPixel(i+1,j+1) == 255) environs ++;
if (environs == 1) {
selectImage(mapExtremaID);
setPixel(i, j, 255);
showSelection=0;
if (showOnlyFinal == 1 && pass == showPassChoice && showExtrema==1 && overlay==1) showSelection=1;
if (showOnlyFinal == 0 && showExtrema==1 && overlay==1) showSelection=1;
if (showSelection == 1 && isOpen (destination)) {
selectImage (destination);
makePoint(i,j);
run("Add Selection...", "stroke=&extremityCoul width=1"); // show extremite as overlay
makeRectangle((i-1), (j-1), 3, 3);
run("Add Selection...", "stroke=&extremityEdgeCoul width=1"); // show extremite as overlay
}
nbExtrema ++;
}
run("Select None");
}
}
}
//mapExtremaID contains the limits
return mapExtremaID;
}
function mapNodes (binID,destination,overlay,keepPreviousMap,calculate) {
//returns mapNodesID which contains the map of the nodes (as 5x5 pixels circular dots)
nbNodes=0; nbJunctions=0; nbMasterJunctions=0;
if (isOpen(mapNodesID) && keepPreviousMap==0) {selectImage (mapNodesID); close();}
if (isOpen (binID)) selectImage (binID); else exit ("no tree image available");
if (isOpen (mapMasterJunctionID)) {selectImage (mapMasterJunctionID); close();}
if (calculate=="MasterNodes") {
getDimensions(width, height, channels, slices, frames);
newImage("map Master Junctions", "8-bit White", width, height, 1);
mapMasterJunctionID = getImageID();
}
selectImage (binID);
nomdArbre=getTitle;
nom="mapNodes";
run("Duplicate...", "title=&nom");
mapNodesID = getImageID();
roiManager("Show None");
run("Remove Overlay");
nom="tempNode";
selectImage (binID);
run("Duplicate...", "title=&tempNode");
tempNodeID=getImageID();
selectImage (mapNodesID);
getDimensions(width, height, channels, slices, frames);
setBackgroundColor (255, 255, 255);
setForegroundColor (0, 0, 0);
run("Select All");
run("Clear", "slice");run("Select None");
j=0;
for (j=0; j<height; j++) {
for (i=0; i<width; i++) {
selectImage(tempNodeID);
environs=0;
snif = getPixel(i,j);
if (snif > 0) {
if (getPixel(i-1,j-1) == 255) environs ++;
if (getPixel(i,j-1) == 255) environs ++;
if (getPixel(i+1,j-1) == 255) environs ++;
if (getPixel(i-1,j) == 255) environs ++;
if (getPixel(i+1,j) == 255) environs ++;
if (getPixel(i-1,j+1) == 255) environs ++;
if (getPixel(i,j+1) == 255) environs ++;
if (getPixel(i+1,j+1) == 255) environs ++;
if (environs > 2) {
selectImage(mapNodesID);
//makeRectangle((i-1), (j-1), 3, 3);
makeOval((i-3), (j-3), 7, 7);
//if (pass == showPassChoice && supressVerySmallSegments == 1) makeOval((i-4), (j-4), 9, 9); //to avoid very small segments due to two near nodes (1 or 2 pixels distant)
run("Fill", "slice");
run("Select None");
showSelection=0;
if (showOnlyFinal == 1 && pass == showPassChoice && showNodes==1 && overlay==1) showSelection=1;
if (showOnlyFinal == 0 && showNodes==1 && overlay==1) showSelection=1;
if (showSelection == 1 && isOpen (destination)) {
selectImage (destination);
//makeRectangle((i-1), (j-1), 3, 3);
makeOval((i-3), (j-3), 7, 7);
if (calculate=="Nodes") run("Add Selection...", "stroke=&nodesCoul width=1 fill=&nodesCoul"); // show nodes as overlay
}
if (calculate=="Nodes") nbNodes ++;
}
run("Select None");
}
}
}
if (isOpen(tempNodeID)) { selectImage (tempNodeID); close ();}
run("Select None");
selectImage (mapNodesID);
nom="mapJunction";
run("Duplicate...", "title=&nom");
mapJunctionID=getImageID();
run("Set Measurements...", "area min perimeter redirect=None decimal=2");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing clear include record");
for (i=0; i< nResults; i++) {
selectImage (mapJunctionID);
doWand(getResult("XStart",i), getResult("YStart",i),0, "8-connected");
if (showSelection == 1 && isOpen (destination)) {
selectImage (destination);
run("Restore Selection");
if (supressVerySmallSegments==1) {run("Enlarge...", "enlarge=0");} else {run("Enlarge...", "enlarge=1");}
if (calculate=="Nodes") {
run("Add Selection...", "stroke=&junctionCoul width=2 "); // show junctions as overlay
run("Select None");
nbJunctions ++;
}
if (calculate=="MasterNodes") {
nbMasterJunctions ++; // number to be recalculated in the final master node map
selectImage (mapMasterJunctionID);
run("Restore Selection");
run("Fill", "slice");
run("Select None");
}
}
selectImage (mapJunctionID);
run("Select None");
}
if (isOpen(mapJunctionID)) { selectImage (mapJunctionID); close ();}
selectImage (mapNodesID);
return mapNodesID;
// mapNodes contains the nodes
}
// for segmentation of the tree
function histoAnalyse(Bright,method) {
// get the auto threshold values
partofHisto=0;histo1=0;
method = method +" dark";
setAutoThreshold(method);getThreshold (lower, upper);
resetThreshold();
// analyse of the histogram:
getStatistics(area, mean, min, max, std, histogram);
vol=newArray(3);
vol[0]=volume (histogram,min,lower);
vol[1]=volume (histogram,lower,upper);
vol[2]=volume (histogram,upper,max);
maxvol=maxOf(vol[1], vol[2]);
for (a=1; a<3; a++) {if (maxvol == vol[a]) partofHisto = a;}
if (partofHisto == 1) histo1=lower;
if (partofHisto == 2) histo1=upper;
setThreshold(histo1, max,"black & white");
run("Convert to Mask");
if (Bright==0) run("Invert");
}
function volume (histo,mini,maxi) {
volhisto=0;
if ((maxi-mini) > 0) {
for (i=mini; i<= maxi; i++) {
volhisto=volhisto +(i* histo[i]);
}
}
return volhisto;
}
function recordTheStepOfLimbing () {
stepID=getImageID();
recordStepOption=1;
step=1;
batchChoice=1;
nomdimage = getTitle;
if (lastIndexOf(nomdimage, sufficAn) > 1) {
workingima = substring (nomdimage,0,lastIndexOf(nomdimage, sufficAn));
} else {workingima=nomdimage;}
nameInitImageorFolder=workingima;
workingImagTemp=nameInitImageorFolder;
windowTabName="Stat Results Table"; nameOfStatTab="["+windowTabName+"]";
if ( !is("binary")) settings ();
binStatus=0;
if ( is("binary")) binStatus =1;
imageFolder=getDirectory("image");
imageFolderStep=imageFolder;
for (stepByStep=-1; stepByStep<= nbIt; stepByStep++) {
if (stepByStep < 0) {
if ( !is("binary")) tree ();
if (is("binary")) q3id=getImageID();
workingImagTemp=workingima;
totreatTemp=getImageID();
if (isOpen(q3id)) {
selectImage(q3id);
titreStep=" pass="+(stepByStep)+"-step"+ (step++);
recordSteps (q3id,workingImagTemp,titreStep);
selectImage(q3id);
}
findLoop (totreatTemp,0);
if (isOpen(q3id)) {
selectImage(q3id);
titreStep=" pass="+(stepByStep)+"-step"+ (step++);
recordSteps (q3id,workingImagTemp,titreStep);
selectImage(q3id);
}
batchChoice=1;
loopIDTemp=getImageID();
batchChoice=1;
findNodesAndBranches ();
batchChoice=1;
imageFolder=imageFolderStep;
if (isOpen(workid)) {
selectImage(workid);
run("Grays");
titreStep=" pass="+(stepByStep)+"-step"+ (step++);
recordSteps (workid,workingImagTemp,titreStep);
selectImage(workid); close ();
}
if (isOpen(q3id)) {
selectImage(q3id);
run("Grays");
titreStep=" pass="+(stepByStep)+"-step"+ (step++);
recordSteps (q3id,workingImagTemp,titreStep);
selectImage(q3id); close ();
}
} else {
showPassChoice=stepByStep;
if ( binStatus== 0) {
selectImage (stepID);
findNodes (1);
} else {
workingima =workingImagTemp;
selectImage (stepID);
rename(workingima);
run("Duplicate...", "title=q3 bis");
q3id=getImageID();
findNodes (0);
}
}
}
recordStepOption=0; batchChoice=0;
}
//setBatchMode("exit and display");
//exit
function recordSteps (toRecordId,toRecordIma,curentStep) {
if (imageFolder !="" && toRecordIma !="" ) {
recordFolderStep = imageFolder + toRecordIma + "=Steps" + File.separator;
recordFolderStepVisu = recordFolderStep + "Visus" + File.separator;
File.makeDirectory(recordFolderStep);
if (!File.exists(recordFolderStep)) exit ("Unable to create the \"" + recordFolderStep + "\"" +" directory.");
File.makeDirectory(recordFolderStepVisu);
if (!File.exists(recordFolderStepVisu)) exit ("Unable to create the \"" + recordFolderStepVisu + "\"" +" directory.");
if (isOpen (toRecordId)) {
selectImage (toRecordId);
run("Flatten");
pathVisu=recordFolderStepVisu + toRecordIma + curentStep + "-visu";
saveAs("PNG",pathVisu);
close();
selectImage (toRecordId);
saveAs("tiff",recordFolderStep + toRecordIma + curentStep);
}
if (isOpen(windowTabName)) {saveTab (recordFolderStep,windowTabName,toRecordIma);}
}
}
// tab for results part
// function building/managing a table window
function TabWindow (addLine) {
// values:
undoErease = "";
if (! isOpen(windowTabName)) {
run("New... ", "name="+nameOfStatTab+" type=Table");
print(nameOfStatTab, "\\Headings:Image Name\tAnalysed area\tNb extrem.\tNb nodes\tNb Junctions\tNb master junction\tNb master segments\tTot. master segments lenght\tNb meshes\tTot.meshes area\tNb peaces\tNb segments\tNb branches\tNb isol. seg.\tTot. lenght\tTot. branching lenght\tTot. segments lenght\tTot. branches lenght\tTot. isol. branches lenght\tBranching interval\tMesh index\tMean Mesh Size\tPath");
}
if (addLine == 0) {print(nameOfStatTab, "\\Clear");}
print(nameOfStatTab, workingima+ "\t" + analyzedArea + "\t" + nbExtrema + "\t" + nbNodes + "\t" + nbJunctions + "\t" + nbMasterJunctionsFinal + "\t" + nbMasterSgment + "\t" + totalMasterSegmentLenght + "\t" + nbMesh + "\t" + totalMeshSize + "\t" + nbTotalPeaces + "\t" + nbSegments+ "\t" + nbTwigs + "\t" +nbIsolated + "\t" + totalLenght + "\t" + totalBranchingLenght + "\t" + totalSegmentsLenght + "\t" + totalTwigsLenght + "\t" + totalIsolatedLenght + "\t" + branchingIndex + "\t" + meshIndex + "\t" + meanMeshSize + "\t" + imageFolder);
}
// function removing the last line of the tab
function rmLastLine () {
if ( isOpen (windowTabName)) {
selectWindow (windowTabName);
tabContent = getInfo();
linesInTab = split(tabContent, "\n");
if (linesInTab[linesInTab.length-1] > 0) {
print(nameOfStatTab, "\\Clear");
resteLines="";
for (i=1; i < (linesInTab.length -1); i++) {
resteLines=resteLines+linesInTab[i] +"\n";
}
if (linesInTab.length > 2) print (nameOfStatTab,resteLines);
if (linesInTab.length > 1) undoErease=linesInTab[linesInTab.length-1];
}
}
}
// function restoring the last ereased line in the table
function undormLastLine () {
if (undoErease != "") print(nameOfStatTab,undoErease);
undoErease="";
}
function openStatResultTable () {
requires("1.39d");
path = File.openDialog("Select a File");
name = File.getName(path);
if (endsWith(name, ".xls")) {name=substring(name, 0, indexOf(name, ".xls"));} else {exit ("This file doesn't seam to be an Excel type file.");}
openTab (path,name);
imageFolder=""; path="";
}
function saveAndCloseAnalysis (closeWin) {
workingImagTemp="";
setBatchMode(true);
if (isOpen (workid)) {
selectImage (workid);
workingImagTemp=getTitle();
}
if (isOpen(singleAnaMapExtID)) {
titreStep="-Map of Extremities";
recordSteps (singleAnaMapExtID,workingImagTemp,titreStep);
if (closeWin==1) {selectImage (singleAnaMapExtID); close ();}
}
if (isOpen(singleAnaMapNodeID)) {
titreStep="-Map of Nodes";
recordSteps (singleAnaMapNodeID,workingImagTemp,titreStep);
if (closeWin==1) {selectImage (singleAnaMapNodeID); close ();}
}
if (isOpen(masterTreeID)) {
titreStep="-Master Tree";
recordSteps (masterTreeID,workingImagTemp,titreStep);
if (closeWin==1) {selectImage (masterTreeID); close ();}
}
if (isOpen(mapMasterTreeID)) {
titreStep="-Map of Master Tree";
recordSteps (mapMasterTreeID,workingImagTemp,titreStep);
if (closeWin==1) {selectImage (mapMasterTreeID); close ();}
}
if (isOpen(initid)) {
titreStep="-init";
recordSteps (initid,workingImagTemp,titreStep);
if (closeWin==1) {selectImage (initid); close ();}
}
if (isOpen(workid)) {
titreStep="";
recordSteps (workid,workingImagTemp,titreStep);
if (closeWin==1) {selectImage (workid); close ();}
}
if (isOpen(q3id)) {
titreStep="-Final Tree";
selectImage (q3id);
run("Remove Overlay");
recordSteps (q3id,workingImagTemp,titreStep);
if (closeWin==1) {selectImage (q3id); close ();}
}
}
function settings () {
Dialog.create("Settings for analysis");
Dialog.addChoice("Kind of objects:", objectsChoices, objectsChoice);
Dialog.show();
objectsChoice = Dialog.getChoice();
if (objectsChoice == objectsChoices[0]) objects = 1;
if (objectsChoice == objectsChoices[1]) objects = 2;
}
function closeAll() {
if (! is("Batch Mode")) {setBatchMode(true);}
if (isOpen (mapExtremaID)) {selectImage (mapExtremaID); close ();}
if (isOpen (mapNodesID)) {selectImage (mapNodesID); close ();}
if (isOpen (q3id)) {selectImage (q3id); close ();}
if (isOpen (workid)) {selectImage (workid); close ();}
if (isOpen (initid)) {selectImage (initid); close ();}
if (isOpen(mapMasterTreeID)) {selectImage (mapMasterTreeID); close();}
if (isOpen(masterTreeID)) {selectImage (masterTreeID); close();}
if (isOpen(mapMasterJunctionID)) {selectImage (mapMasterJunctionID); close();}
if (isOpen(singleAnaMapExtID)) {selectImage (singleAnaMapExtID); close();}
if (isOpen(singleAnaMapNodeID)) {selectImage (singleAnaMapNodeID); close();}
if (isOpen(initSkeleton)) {selectImage (initSkeleton); close();}
}
// saving a tab as excel type file
function saveTab (path,WinTab,nameinit) {
if (isOpen(windowTabName)) {
if (path == "--" || path =="") {
selectWindow (windowTabName);
run("Input/Output...", "jpeg=75 gif=-1 file=.xls");
saveAs("Text");
}
if (path != "--") {
selectWindow(windowTabName);
thepath = path+nameinit+"-"+WinTab+".xls";
if (WinTab != "Stat Results Table") {
thepath = path+ WinTab + ".xls";
} else
if (nameinit == "") {
thepath = path+nameinit + WinTab +".xls";
} else {
thepath = path+nameinit+"-"+WinTab +".xls";
}
}
saveAs("Text", thepath);
} else {exit ("No Stat Results Table. Tab files have to be opened or generated by the Angiogenesis Analyzer");}
}
function openTab (path,name) {
undoErease="";windowTabName=name; workingima="";
lines=split(File.openAsString(path), "\n");
if (lines.length < 2) { exit ("This file doesn't seam to contain data");}
headings = lines[0];
titlesOfColumns = split(headings, ",\t");
nameOfStatTab="["+windowTabName+"]";
if (isOpen(windowTabName)) {selectWindow(windowTabName) ;run("Close");}
firstLine="";
for (i=0; i < (titlesOfColumns.length ); i++) {
firstLine=firstLine+ titlesOfColumns [i];
if ( i < (titlesOfColumns.length )-1) {firstLine=firstLine+ "\t";}
}
toPrint="";
for (i=1; i < (lines.length ); i++) {
toPrint=toPrint+lines[i]+"\n";
}
run("New... ", "name="+nameOfStatTab+" type=Table");
print(nameOfStatTab, "\\Headings:"+firstLine+"");
print(nameOfStatTab,toPrint);
}
// batch processing adapter:
function batchProcessing () {
selectedDir = getDirectory("Choose a Directory ");
nameInitImageorFolder = File.getName(selectedDir);
setBatchMode(true);
settings ();
workingImagTemp="";
windowTabName ="Stat Results Table";
nameOfStatTab="["+windowTabName+"]";// ajuster le nom avec le nom de dossier master
if (isOpen(windowTabName)) {print(nameOfStatTab, "\\Clear");}
countBatch = 0; // number of file to analyse
countFiles(selectedDir);
incremcountBatch = 0;fileProcessed=""; countBatchTreated=0;
starttime = getTime();
if (countBatch > 0) {
showMessageWithCancel (countBatch + " Image(s) will be processed");
if (isOpen(batchStatusWindow)) {print(batchStatus, "\\Clear");}
processFiles(selectedDir);
fileProcessed=fileProcessed + "Nb image(s) processed="+countBatchTreated+ ". Processing time= "+ HMS (getTime-starttime) ;
saveTab (selectedDir,windowTabName,nameInitImageorFolder);
} else {exit ("No .tiff file found");}
}
// count the number of file to process according to criteria, image suffix, folder name suffix, file type ?
function countFiles(selectedDir) {
list = getFileList(selectedDir);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/") && ! endsWith(list[i], TreatedFolderSuffix)) {
countFiles(""+selectedDir+list[i]);
} else {
path = selectedDir+list[i];
if (endsWith(path, ext1) || endsWith(path, ext2)) {
countBatch++;
}
}
}
}
function processFiles(selectedDir) {
list = getFileList(selectedDir);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/") && ! endsWith(list[i], TreatedFolderSuffix)){
processFiles(""+selectedDir+list[i]);
} else {
showProgress(incremcountBatch++, countBatch);
path = selectedDir+list[i];
if (endsWith(path, ext1) || endsWith(path, ext2)) {
countBatchTreated++;
processFile(path,1);
call("java.lang.System.gc"); // empty the garbage memomry
print ("\\Clear");
fileProcessed=fileProcessed + path+ "\n";
// built the progess batch window
if (!isOpen(batchStatusWindow)) {run("New... ", "name="+batchStatus+" type=Table");}
print(batchStatus, "\\Clear");
print(batchStatus, fileProcessed);
meanTime=(getTime-starttime)/countBatchTreated;
timeRemaining=(countBatch-countBatchTreated)*meanTime;
print(batchStatus, countBatchTreated + " image(s) processed on " + countBatch);
print(batchStatus, "Performed processing time: " + HMS (getTime-starttime));
print(batchStatus, "Mean processing time per image= " + HMS (meanTime));
if ((countBatch-countBatchTreated) != 0) print(batchStatus, "Estimated processing time remaining: " + HMS (timeRemaining));
if (isOpen(batchStatusWindow)) {
selectWindow (batchStatusWindow);
setLocation(0, (ecranY/2));
}
}
}
}
}
function HMS (milliSec) {
seconds = milliSec/1000;
Shours= (floor (seconds/3600));
Sminutes= floor ((seconds-(3600*Shours)) /60);
Sseconds= d2s ((seconds-(3600*Shours)-(60*Sminutes)),2);
theTime=toString(Shours) + " h " + toString(Sminutes) + " min "+ toString(Sseconds) + " sec";
return theTime;
}
function processFile(path,saveOption) {
open(path);
folderpath=getDirectory("image");
returnedImageID=Treatment();
if (saveOption ==1) {
format="tiff";
if (onFoldeByImage==1) {
folderTreatedpath=folderpath + imageName + TreatedFolderSuffix +File.separator; // on folder for each image
}
if (onFoldeByImage==0) {
foldername=File.getName(folderpath);
folderTreatedpath=folderpath + foldername + TreatedFolderSuffix +File.separator; // on folder for all images
}
File.makeDirectory(folderTreatedpath);
if (!File.exists(folderTreatedpath)) exit ("Unable to create the \"" + folderTreatedpath + "\"" +" directory.");
selectImage(returnedImageID);nom = getTitle;
if (folderTreatedpath != "") {
if (isOpen (workid)) {
selectImage (workid);
saveAs (format, folderTreatedpath+nom);
pathVisu=folderTreatedpath+nom+"-visu";
run("Flatten");
saveAs("jpeg",pathVisu);
close();
}
}
}
closeAll (); // for residual analysis images
}
// Image treatment function
function Treatment() {
analysedID=findNodes (1);
return analysedID;
}
macro "Hide overlay [h]" {
run("Hide Overlay");
}
macro "Show overlay [s]" {
run("Show Overlay");
}
// for blinking to evaluate the pertinancy
macro "Blink overlay [b]" {
blinkOverlay () ;
}
function blinkOverlay () {
source=getImageID();
blink (source);
}
function blink (image) {
selectImage (image);
start = getTime;
while (click()==0 && (getTime-start)<4000) {
wait(500);click();run("Hide Overlay");
wait(500);run("Show Overlay");
}
}
// adapted from the GetCursorLocDemo macro available at the
// http://rsb.info.nih.gov/ij/macros/GetCursorLocDemo.txt
function click() {
rightButton=4;leftButton=16;
getCursorLoc(x, y, z, flags);
if (flags&leftButton!=0) exit;
if (flags&rightButton!=0) exit;
return 0;
}
// additional utilities
function aboutTheTools () {
requires("1.46i");
about="--------------------------- \"Angiogenesis Analyzer\" ------------------------------\n\n";
about= about+"This set of tools allows analysis of cellular networks. Typically it can detect and analyze the\n";
about= about+"pseudo vascular organization of endothelial cells cultured in gel medium.\n";
about= about+"Version 1.0.a for numerical support of 2012 edition of the ImageJ Conferences, Luxembourg.\n";
about= about+"\n";
about= about+"------------------------------------------------------------------------------\n";
about= about+"Installation: the tools file has to be stored in the \"ImageJ/macros/toolset\" repertory \n";
about= about+"------------------------------------------------------------------------------\n";
about= about+"Short documentation:\n\n";
about= about+"- \" Network Analysis Menu Tool\" provides functions to analyze phase contrast and fluorescent\n";
about= about+" images of endothelial cell networks.\n";
about= about+"- \" Blurred Mask Tool\" removes the gradient in a selected area, useful to remove aggregates of\n";
about= about+" dirt in phase contrast images.\n";
about= about+"- \" Tuning Functions Menu Tool\" regroups a series of functions to test each step of analysis \n";
about= about+" the best settings for a new image origin. It also provides a tool to get \n";
about= about+" customized overlays of detected elements.\n";
about= about+"- \" Batch Image Treatment Tool\" allows analysis of batch of images in several level of directories.\n";
about= about+" The function records individual results summarized in a table as an Excel like file and\n";
about= about+" analyzed images containing the detected elements as overlay.\n";
about= about+"- \" Measurement Documents Menu Tool\" regroups functions to open, edit and save the result\n";
about= about+"- \" Online Documentation and Demo\" tool bar menu gives some internet resources including\n";
about= about+" online documentation and downloadable images samples.\n";
about= about+"- \" Version and Update Information\" tool bar menu provides version and update information.\n";
about=about + "\n------------------------------------------------------------------------------";
about=about +"\nAuthor : Gilles Carpentier"+"\nFaculte des Sciences et Technologie"+"\nUniversite Paris Est Creteil Val de Marne, France.";
about=about + "\n------------------------------------------------------------------------------\n";
// from PrintToTextWindow macro available at the http://rsbweb.nih.gov/ij/macros/PrintToTextWindow.txt
// author: Wayne Rasband
title1 = "Infos for the \"Angiogenesis Analyzer\"";
title2 = "["+title1+"]";
f = title2;
if (isOpen(title1)) {
print(f, "\\Update:"); // clears the window
print(f, about);
selectWindow (title1);
} else {
run("New... ", "name="+title2+" type=[Text File] width=80 height=16");
print(f, about);
}
}
function netTest () {
if (indexOf (File.openUrlAsString(urllist), errorNetMessage) >0) exit("You need an internet access to run this function.");
}
function doc () {
netTest ();
showMessageWithCancel ("A notice is avaible on line. Open it with your default web browser?");
run("URL...", "url=["+onlinedoclink +"]");
}
function OpenImageLink(link,name,question) {
// Check if already downloaded.
demoimalocation = getDirectory("startup");
fildestination = demoimalocation+ "Downloaded Demo Images/" + name;
if (File.exists(fildestination)) {
if (question ==1 ) showMessageWithCancel ("The \"" + name + "\" has already been downloaded. Open it?");
open(fildestination);
}
else {
netTest ();
showMessageWithCancel ("ImageJ will download a demo image. Continue?");
run("URL...", "url=["+link+"]");
imageid = getImageID();
nomdimage = getTitle;
// Create a <Downloaded Demo Images> repertory in ImageJ folder.
ImaDemo = demoimalocation+"Downloaded Demo Images"+File.separator;
File.makeDirectory(ImaDemo);
if (!File.exists(ImaDemo)) exit("Unable to create directory, something wrong in the ImageJ folder");
selectWindow(nomdimage);
save(""+ImaDemo+""+ nomdimage +"");
}
}
////// end addition utilities
// -------------------*** Additionnal code for on line update resources ***-----------------------------
//Developer info
//Kind:Toolset
//Title:"Angiogenesis Analyzer"
//Version:1.0.c
//Date: 03 Dec 2013
//Origin:NIH
//NotUpdateThisFile
//End info
function VersionInfos () {
// variables for on line update resources
beginsign="//Developer info";endsign="//End info";
kind="toolsets/";
urlrep="http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/";
name="Angiogenesis Analyzer.txt";
namedev="Angiogenesis Analyzer.txt";
favoritefoldername= "Macros";
version=versionMessage();
if (indexOf(version, "install it?" ) > 0 ) {
macrotext=getdistantmacro (namedev,urlrep);macrolocal="";
macropath=getDirectory("macros")+kind+namedev;
if (File.exists(macropath)) {macrolocal=File.openAsString(macropath);}
if (macrotext != macrolocal) {
//perfom the installation
Dialog.create("New version installation option");
Dialog.addMessage(version);
Dialog.addCheckbox("Install a Plugin Shortcut?", 0);
Dialog.addMessage("(This option provides a shortcut in the plugins menu of ImageJ, making easier\nthe next use of the new installed version).");
Dialog.show();
plugin= Dialog.getCheckbox();
f= File.open(macropath);
print (f,macrotext);
File.close(f);
if (plugin ==1) {InstallPluginsStarter(namedev);}
message="The installation of the "+giveDevInfo (macrotext,1)+ " "+ giveDevInfo (macrotext,2)+ "is completed.";
message=message+ " Do you want to run it?";
showMessageWithCancel(message);
run("Install...", "install=["+macropath+"]");
}
} else {showMessage (version);}// comment without installation available
}
function versionMessage() {
version="";
if (getDirectory("startup") == 0) exit ("Unable to find the startup directory, something wrong in the ImageJ folder");
if (getDirectory("macros") == 0) exit ("Unable to find the macros directory, something wrong in the ImageJ folder");
MacroPath=getDirectory("macros");thismacropath=MacroPath+kind+name;
if (! File.exists(thismacropath)) exit ("This macro has to be recorded under the name of \"" +name+"\"\ninto the \"macros/"+kind+"\" folder of ImageJ.");
macrotext=File.openAsString(thismacropath);
macrotextdistant=getdistantmacro (namedev,urlrep);
version="";macrolocal="";
version=version + "\n \nThis version of the " + giveDevInfo (macrotext,1) + " " + giveDevInfo (macrotext,2);
version=version + "is provided by the " + giveDevInfo (macrotext,5)+ " web site.";
version=version + "\nVersion number: " + giveDevInfo (macrotext,3)+ " - " + giveDevInfo (macrotext,4) +".";
if (macrotextdistant !="" ) {
new=giveDevInfo (macrotextdistant,3);old=giveDevInfo (macrotext,3);
if (new > old) {
macropath=getDirectory("macros")+kind+namedev;
if (File.exists(macropath)) {macrolocal=File.openAsString(macropath);}
if (macrotextdistant != macrolocal) {
update="\n \nA new version "+new+ " is available on the " +giveDevInfo (macrotextdistant,5)+ " web site: ";
update=update+ "\n \nDo you want to install it?";
} else {
update ="\n \nThe latest "+new+" version called \"" +namedev+ "\" provided by \nthe "+giveDevInfo (macrotextdistant,5) +" web site has already be installed";
update = update+ " in the \"" +kind+ "\" repertory \nof ImageJ.";
}
} else {
update="No new version available.";
}
version=version +"\n" + update ;
}
return version;
}
function giveDevInfo (text,n) {
lines=split(text,"\n");
if ( (indexOf(text, beginsign)<0) || (indexOf(text, endsign)<0) ) exit ("Not upgradable macro code.");
for (i=0; lines[i] != endsign; i ++) {}
for (j=i; lines[j] != beginsign; j --) {}
infotext=newArray(i-j-1);
for (i=0; i < infotext.length; i ++) {infotext[i]=lines[i+j+1];}
info=infotext[n-1]; signature=":";
cut = indexOf(info, signature);
info = substring(info,(cut+lengthOf(signature)),lengthOf(info));
return info;
}
// Function giving the content of a distant macro (name) located at the distant repertory (urlrep).
function getdistantmacro (name,urlrep) {
macrotextnih="";
erNetMessage ="Error: ";
testlink = "http://rsb.info.nih.gov/ij/macros/Arrays.txt";
if (indexOf (File.openUrlAsString(testlink), erNetMessage) < 0) {
distantmacrolink = urlrep + name;
if (indexOf(distantmacrolink, " ") > -1) {
while (indexOf(distantmacrolink, " ") > -1) {
distantmacrolink=substring(distantmacrolink, 0, (indexOf(distantmacrolink, " ")))+"%20"+substring(distantmacrolink, (indexOf(distantmacrolink, " ")+1),lengthOf(distantmacrolink) );
}
}
showStatus("Internet link...");
macrotextnih =File.openUrlAsString(distantmacrolink);
showStatus("");
} else { showMessage ("No internet connection to looks for new version.");}
return macrotextnih;
}
function InstallPluginsStarter(macroname) {
// from MacroPluginShortcutsTool.txt
codestarter = "run\(\"Install...\", \"install=[\"+getDirectory(\"macros\")+\""+kind+ macroname + "\]\"\);";
if (getDirectory("plugins") == "") exit ("Unable to find the Plugins directory; something wrong in the ImageJ folder.");
if (endsWith(macroname, ".txt") || endsWith(macroname, ".ijm")) pluginname = substring(macroname, 0, (lengthOf(macroname)-4));
StarterDir = getDirectory("plugins")+favoritefoldername+File.separator;
File.makeDirectory(StarterDir);
if (!File.exists(StarterDir)) exit ("Unable to create "+favoritefoldername+" Macros directory, something wrong in the ImageJ folder.");
starterplugin = StarterDir + pluginname +"_ .ijm";
f= File.open(StarterDir + pluginname +"_ .ijm");
print (f,codestarter);
File.close(f);
showMessage ("The plugin shortcut \"" +pluginname+ "\" will be available after\nImageJ restarting, in the \"Plugins->" + favoritefoldername + "\" menu.");
}
// *** End of additionnal code for on line update ressources ***
====================================