From 7adc25cc5c062fece43358bb5d581238f5ce91c2 Mon Sep 17 00:00:00 2001
From: mjthreesixfive <jones1.matthew@gmail.com>
Date: Wed, 27 Jul 2016 08:38:39 +0100
Subject: [PATCH 1/3] Add blue channel text file output

Added text file output for blue channel (not tested!)
---
 nucleus-and-locus-tag-segmentation.ijm | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/nucleus-and-locus-tag-segmentation.ijm b/nucleus-and-locus-tag-segmentation.ijm
index 76a95c2..87c4365 100644
--- a/nucleus-and-locus-tag-segmentation.ijm
+++ b/nucleus-and-locus-tag-segmentation.ijm
@@ -1,3 +1,4 @@
+@@ -0,0 +1,145 @@
 //This macro takes a 3 channel tif cropped to contain just one nucleus
 //It loops through a folder containing many slices and detects several features
 //First it makes a binary image of the DNA in the Blue channel
@@ -69,7 +70,7 @@ for (i=0; i<list.length; i++){
 
 // save the blue channel mask
   		saveAs("Tiff", bdir+w2+"-M1.tif"); 
-
+        saveAs("Text", bdir+w2+"-M1.txt"); 
 //create a ROI from the binary image
 		run("Create Selection");	
 //measure selection
@@ -140,6 +141,3 @@ for (i=0; i<list.length; i++){
 }
 setBatchMode(false); //exit batch mode
 print(dir1+" analysis finished");
-
-
-

From 145c2991a5dc4752fcff6c1fe17919f09405b62b Mon Sep 17 00:00:00 2001
From: mjthreesixfive <jones1.matthew@gmail.com>
Date: Wed, 27 Jul 2016 08:41:15 +0100
Subject: [PATCH 2/3] Fixed accidental header

removed top line which was copied by mistake.
---
 nucleus-and-locus-tag-segmentation.ijm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nucleus-and-locus-tag-segmentation.ijm b/nucleus-and-locus-tag-segmentation.ijm
index 87c4365..8d8a31c 100644
--- a/nucleus-and-locus-tag-segmentation.ijm
+++ b/nucleus-and-locus-tag-segmentation.ijm
@@ -1,4 +1,3 @@
-@@ -0,0 +1,145 @@
 //This macro takes a 3 channel tif cropped to contain just one nucleus
 //It loops through a folder containing many slices and detects several features
 //First it makes a binary image of the DNA in the Blue channel

From 831c1ab6ae8875abfe668d5bd293a2021eb5ab5d Mon Sep 17 00:00:00 2001
From: mjthreesixfive <jones1.matthew@gmail.com>
Date: Wed, 27 Jul 2016 08:44:05 +0100
Subject: [PATCH 3/3] Fixed wrong command

changed 'Text' to 'Text Image' - correct command for text output.
---
 nucleus-and-locus-tag-segmentation.ijm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nucleus-and-locus-tag-segmentation.ijm b/nucleus-and-locus-tag-segmentation.ijm
index 8d8a31c..07c1d8c 100644
--- a/nucleus-and-locus-tag-segmentation.ijm
+++ b/nucleus-and-locus-tag-segmentation.ijm
@@ -69,7 +69,7 @@ for (i=0; i<list.length; i++){
 
 // save the blue channel mask
   		saveAs("Tiff", bdir+w2+"-M1.tif"); 
-        saveAs("Text", bdir+w2+"-M1.txt"); 
+        saveAs("Text Image", bdir+w2+"-M1.txt"); 
 //create a ROI from the binary image
 		run("Create Selection");	
 //measure selection