fixed bug to account for channel number when using hu for ganglia

pr4deepr · Mar 21, 2022 · 0f01ac9 · 0f01ac9
1 parent 1928f2e
commit 0f01ac9
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Showing 2 changed files with 26 additions and 3 deletions.
diff --git a/_Analyse Neuron (Multi-channel).ijm b/_Analyse Neuron (Multi-channel).ijm
@@ -284,7 +284,7 @@ if(ganglia_channel!="NA")
 //Array.show(marker_names_manual);
 //Array.show(marker_no_manual);
 //exit("test");
-if(sizeC>1)
+if(sizeC>1 && Ganglia_detection!="Define ganglia using Hu")
 {
  if (Cell_counts_per_ganglia==true && cell_channel=="NA" && ganglia_channel=="NA") //count cells per ganglia but don't know channels for ganglia or neuron
 	{
@@ -326,7 +326,18 @@ if(sizeC>1)
 	}
 
 }
-
+else if(Ganglia_detection=="Define ganglia using Hu" && cell_channel=="NA")
+{
+	waitForUser("Note the channels for "+cell_type+" and enter in the next box.");
+	Dialog.create("Choose  channel for "+cell_type+);
+	Dialog.addNumber("Enter "+cell_type+" and ganglia channel", 3);
+	Dialog.show(); 
+	cell_channel= Dialog.getNumber();
+	ganglia_channel = cell_channel;
+	Stack.setChannel(cell_channel);
+	resetMinAndMax();
+}
+else  if(Ganglia_detection=="Define ganglia using Hu") ganglia_channel = cell_channel;
 else exit("Need multiple channels, only one channel found");
 
 

diff --git a/_Analyse Neurons (Hu only).ijm b/_Analyse Neurons (Hu only).ijm
@@ -203,7 +203,7 @@ if(cell_channel!="NA")
 
 
 //if more than one channel , check if appropriate values entered
-if(sizeC>1)
+if(sizeC>1 && Ganglia_detection!="Define ganglia using Hu")
 {
  if (Cell_counts_per_ganglia==true && cell_channel=="NA" && ganglia_channel=="NA") //count cells per ganglia but don't know channels for ganglia or neuron
 	{
@@ -252,6 +252,18 @@ if(sizeC>1)
 	}
 
 }
+else if(Ganglia_detection=="Define ganglia using Hu" && cell_channel=="NA")
+{
+	waitForUser("Note the channels for "+cell_type+" and enter in the next box.");
+	Dialog.create("Choose  channel for "+cell_type+);
+	Dialog.addNumber("Enter "+cell_type+" and ganglia channel", 3);
+	Dialog.show(); 
+	cell_channel= Dialog.getNumber();
+	ganglia_channel = cell_channel;
+	Stack.setChannel(cell_channel);
+	resetMinAndMax();
+}
+else  if(Ganglia_detection=="Define ganglia using Hu") ganglia_channel = cell_channel;
 else cell_channel = 1;