From 5c08213bd087cc849023e0e1096698516fa6784e Mon Sep 17 00:00:00 2001
From: "Shao-Chun, Peggy, Hsu" <67047201+peggyscshu@users.noreply.github.com>
Date: Wed, 25 Nov 2020 18:00:03 +0800
Subject: [PATCH] Add files via upload

---
 Batch assy in oil red.ijm | 140 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 140 insertions(+)
 create mode 100644 Batch assy in oil red.ijm

diff --git a/Batch assy in oil red.ijm b/Batch assy in oil red.ijm
new file mode 100644
index 0000000..9289a19
--- /dev/null
+++ b/Batch assy in oil red.ijm	
@@ -0,0 +1,140 @@
+//Set Batch
+   dir = getDirectory("Choose a Directory ");
+   Table.create("Oil red analysis");
+   setBatchMode(true);
+   count = 0;
+   countFiles(dir);
+   n = 0;
+   processFiles(dir);
+   
+   function countFiles(dir) {
+      list = getFileList(dir);
+      for (i=0; i<list.length; i++) {
+          if (endsWith(list[i], "/"))
+              countFiles(""+dir+list[i]);
+          else
+              count++;
+      }
+    }
+    //print(count);
+    
+    function processFiles(dir) {
+      list = getFileList(dir);
+      for (i=0; i<list.length; i++) {
+          if (endsWith(list[i], "/"))
+              processFiles(""+dir+list[i]);
+          else {
+             showProgress(n++, count);
+             path = dir+list[i];
+             processFile(path);
+          }
+      }
+   	}
+
+  		function processFile(path) {
+       		if (endsWith(path, ".tif")) {
+           		open(path);
+           		oilred();
+       		}
+  		}
+
+		function oilred(){
+			//IO
+				tifName = getTitle();
+				folderName = replace(tifName, ".tif", "");
+				dir1parent = File.directory;
+				dir2 = dir1parent+File.separator+folderName ;
+				if (File.exists(dir2)==false) {
+					File.makeDirectory(dir2);
+				}
+			//Prepare for analysis
+	    		run("Set Scale...", "distance=0 known=0 unit=pixel global");
+				selectWindow(tifName);
+				rename("Raw");
+				run("Duplicate...", "title=Tissue");
+				selectWindow("Raw");
+				run("Colour Deconvolution", "vectors=[User values] [r1]=0.748963 [g1]=0.6062903 [b1]=0.26733226 [r2]=0.099971585 [g2]=0.73738605 [b2]=0.6680326 [r3]=0.00000 [g3]=0.00000 [b3]=0.00000");//B from FastBlue, R from Masson Trichrome
+				selectWindow("Raw-(Colour_3)");
+				close();
+				selectWindow("Colour Deconvolution");
+				close();
+				selectWindow("Raw");
+				close();
+				selectWindow("Raw-(Colour_1)");
+				close();
+				selectWindow("Raw-(Colour_2)");
+				rename("Oil red");
+			//Measure oil red
+				selectWindow("Oil red");
+				run("Invert");
+				run("Grays");
+				setThreshold(37, 255);
+				run("Analyze Particles...", "display summarize add");
+				run("Summarize");
+				n = nResults(); // n = AP no + 4 statistics
+				if(n>1){
+					c = n-4; // c = AP no
+					nmean = n-4; // where the mean value locates
+					a = getResult("Area",nmean);
+					b = getResult("IntDen", nmean);
+					OrAreaSum = a * c;
+					OrIntSum = b *c;
+				}
+				else{
+					a = getResult("Area",0);
+					b = getResult("IntDen",0);
+					OrAreaSum = a;
+					OrIntSum = b;
+				}
+				
+				/*
+				print("APno  " + c);
+				print("APno + statistics  " + n);
+				print("mean index  " + nmean);
+    			print("OrAreaMean  " + a);
+    			print("OrIntDenMean  " + b);
+    			print("OrAreaSum  " + OrAreaSum);
+    			print("OrIntDenSum  " + OrIntSum);
+				*/
+				roiManager("Save", dir2+File.separator+"oilred.zip");
+				roiManager("Delete");
+				selectWindow("Oil red");
+				close();
+				run("Clear Results");
+			//Measure tissue area
+				selectWindow("Tissue");
+				run("8-bit");
+				setThreshold(0, 237);
+				run("Analyze Particles...", "display summarize add");
+				run("Summarize");
+				n = nResults(); // n = AP no + 4 statistics
+				if (n>1) {
+					c = n-4; // c = AP no
+					nmean = n-4; // where the mean value locates
+					d = getResult("Area",nmean); 
+					TsAreaSum = d * c;
+				}
+				else{
+					TsAreaSum = getResult("Area",0); 
+				}
+    			/*
+				print("APno  " + c);
+				print("APno + statistics  " + n);
+				print("mean index  " + nmean);
+				print("TsAreaMean  " + d);
+				print("TsAreaSum  " + TsAreaSum);
+				*/
+				roiManager("Save", dir2+File.separator+"tissue.zip");
+				roiManager("Delete");
+				selectWindow("Tissue");
+				close();
+				run("Clear Results");
+			//Give result
+				OrPerTs=OrAreaSum*100/TsAreaSum;
+				//print(tifName + ";" + OrPerTs+ ";" + OrIntSum);
+				selectWindow("Oil red analysis");
+				Table.set("File Name", i, tifName);
+				Table.set("Oil red in Tissue area (%)", i, OrPerTs);
+				Table.set("Oil red intensity sum", i, OrIntSum);
+	}
+	
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