Update Script Parameters for IJ update compatibility

BigDecimal updated to Float
lahammond · Jan 6, 2022 · 9d97d0d · 9d97d0d
1 parent e07ce11
commit 9d97d0d
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Showing 7 changed files with 17 additions and 11 deletions.
diff --git a/BrainJ-1.0.5.jar b/BrainJ-1.0.5.jar
diff --git a/BrainJ-1.0.4.jar → Previous Releases/BrainJ-1.0.4.jar b/BrainJ-1.0.4.jar → Previous Releases/BrainJ-1.0.4.jar
diff --git a/pom.xml b/pom.xml
@@ -13,7 +13,7 @@
 	</parent>
 
 	<groupId>com.zuckerman.cellularimaging</groupId>
-	<version>1.0.4</version>
+	<version>1.0.5</version>
 
 	<name>BrainJ</name>
 	<url>https://zuckermaninstitute.columbia.edu</url>
@@ -24,7 +24,7 @@
 	</organization>
 	<licenses>
 		<license>
-			<name>Simplified BSD License</name>
+			<name>MIT License</name>
 			<distribution>repo</distribution>
 		</license>
 	</licenses>

diff --git a/src/main/resources/scripts/Plugins/BrainJ/1_Set_Experiment_Parameters.ijm b/src/main/resources/scripts/Plugins/BrainJ/1_Set_Experiment_Parameters.ijm
@@ -3,6 +3,12 @@
 // First open input directory and check for parameter file
 
 // Potential update: if parameter file exists - populate all the variables - if not then just proceed
+
+
+
+
+//#@ String (visibility=MESSAGE, value="<html><h1><font size=6 color=#0E6655>Cellular Imaging Platform</h><br/><h1><font size=5 color=#154360><i>Zuckerman Institute, Columbia University</i></h1><h3><font size = 4><a href=http://cellularimaging.org/> Cellular Imaging Platform</a></html>") doc
+
 
 #@ File(label="Select folder:", description="Subfolder containing brain raw data", style="directory") input
 
@@ -16,8 +22,8 @@
 #@ String(label="Order of sections on slide:", choices={"Right and Down", "Left and Down", "Right", "Left", "Right and Up", "Left and Up" }, style="listBox", description="Right and Down = Top: 1, 2, 3 Bottom: 4, 5, 6 || Left and Down = Top: 3, 2, 1 Bottom: 6, 5, 4 || Right = 1, 2, 3") SliceArrangement
 
 
-#@ BigDecimal(label="Lateral (XY) resolution of input (um):", value = 1, style="spinner") InputRes
-#@ BigDecimal(label="Final resolution of image output (um/px):", value = 2.00, description="Leave as 0 for original resolution", style="spinner") FinalResolution
+#@ Double(label="Lateral (XY) resolution of input (um):", value = 1, style="spinner") InputRes
+#@ Double(label="Final resolution of image output (um/px):", value = 2.00, description="Leave as 0 for original resolution", style="spinner") FinalResolution
 #@ Integer(label="Section cut thickness (um):", value = 50, style="spinner") ZCut
 
 #@ String(label="Counterstain channel (e.g. DAPI or NeuroTrace):", choices={"1", "2", "3", "4", "5"}, style="radioButtonHorizontal", value = "2", description="Select the channel number containing DAPI or Autofluorescence, to be used for registration.") AlignCh

diff --git a/src/main/resources/scripts/Plugins/BrainJ/2_Reformat_Sections_(Batch_Process).ijm b/src/main/resources/scripts/Plugins/BrainJ/2_Reformat_Sections_(Batch_Process).ijm
@@ -34,8 +34,8 @@
 //Image coordinates can be extracted from Nikon ND2 files for automated reordering of sections, otherwise alphanumeric filenames can be used. <br> <br> "
 
 
-BrainJVer ="BrainJ 1.0.4";
-ReleaseDate= "November 17, 2021";
+BrainJVer ="BrainJ 1.0.5";
+ReleaseDate= "January 6, 2021";
 
 // Initialization
 requires("1.52p");

diff --git a/src/main/resources/scripts/Plugins/BrainJ/4_Set_Analysis_Settings.ijm b/src/main/resources/scripts/Plugins/BrainJ/4_Set_Analysis_Settings.ijm
@@ -40,7 +40,7 @@ TransVolumeTrim = 15;
 #@ Integer(label="Minimum intensity threshold:", value = 125, style="spinner") MaximaInt3
 #@ Integer(label="Minimum cell area (um):", value = 20, style="spinner") Size3
 //#@ Integer(label="Unsharp Mask radius (px, 0 if none):", value = 2, style="spinner") USRad
-//#@ BigDecimal(label="Unsharp Mask weight:", value = 0.700, style="spinner") USMW
+//#@ Double(label="Unsharp Mask weight:", value = 0.700, style="spinner") USMW
 //#@ boolean(label="Measure intensity of each cell:", description="Leave off to save time. Enable to measured mean intensity of each channel for all detected cells.") MeasureInt
 //#@ boolean(label="Display cell intensity on cell validation images:", description="Leave off to save time. Enable to see measured mean intensity overlayed on validation image.") IntVal
 
@@ -58,8 +58,8 @@ TransVolumeTrim = 15;
 
 
 // SETTINGS FOR CHANGING RESOLUTION OF PROJECTION ANALYSIS - CURRENTLY ONLY 25um POSSIBLE BUT COULD DO THIS AT HIGHER RES WITH SOME MODIFICATION - LEAVE OFF OUT FOR V7
-#@ BigDecimal(label="XY resolution used for projection density analysis (um/px):", value = 10.00, description="Higher resolution requires more RAM", style="spinner") ProDetectionResolution
-//#@ BigDecimal(label="Section thickness/resolution used for projection density analysis (default 25) (um):", value = 25.00, description="Leave at 25um unless you are using sections thinner than 25um", style="spinner") ProDetectionResolutionZ
+#@ Double(label="XY resolution used for projection density analysis (um/px):", value = 10.00, description="Higher resolution requires more RAM", style="spinner") ProDetectionResolution
+//#@ Double(label="Section thickness/resolution used for projection density analysis (default 25) (um):", value = 25.00, description="Leave at 25um unless you are using sections thinner than 25um", style="spinner") ProDetectionResolutionZ
 
 #@String  (visibility="MESSAGE", value="   ") out
 #@String  (visibility="MESSAGE", value="--------------------------------------------------------------------------------------------------------------------------------------------------------------") out5

diff --git a/...in/resources/scripts/Plugins/BrainJ/5_Registration_and_Atlas_Analysis_(Batch_Process).ijm b/...in/resources/scripts/Plugins/BrainJ/5_Registration_and_Atlas_Analysis_(Batch_Process).ijm
@@ -17,8 +17,8 @@ run("Colors...", "foreground=white background=black selection=yellow");
 run("Clear Results"); 
 run("Close All");
 
-BrainJVer ="BrainJ 1.0.4";
-ReleaseDate= "November 17, 2021";
+BrainJVer ="BrainJ 1.0.5";
+ReleaseDate= "January 6, 2021";
 
 
 #@ File[] listOfPaths(label="Select experiment/brain folders:", style="both")