16bit converter

README.md

@@ -19,3 +19,5 @@ Grid/Collection Stiching version: 1.2
 
 [issue](https://forum.image.sc/t/converting-16-bit-signed-tiffs-to-16-bit-unsigned/5847/3) signed vs unsigned 16 bit images
 
+## Microscopy Image Stitching Tool (MIST)
+[MIST](https://github.com/USNISTGOV/MIST/wiki/Install-Guide)
\ No newline at end of file

ScanImageStitching.ijm

@@ -50,40 +50,63 @@ function checkPathSeparator(path)
 }
 
 
+/* convert signed to unsigned 16bit
+ * scales between min and max value
+ * requires open stack
+ */
+function convertSignedToUnsigned16bit()
+{
+    run("32-bit");
+    for (s = 1; s <= nSlices; s++) {
+        setSlice(s);
+        getStatistics(area, mean, pixelMin, pixelMax);
+        run("Subtract...", "value=" + pixelMin);
+        setMinAndMax(0, 65535);
+    }
+
+    run("16-bit");    
+    for (s = 1; s <= nSlices; s++) {
+        setSlice(s);
+        getStatistics(area, mean, pixelMin, pixelMax);
+        setMinAndMax(pixelMin, pixelMax);
+    }
+}
+
+
+/* export each image from a stack
+ * prepends stack index to filename
+ * @param export path
+ */
+function exportStackToImages(path)
+{
+    path = checkPathSeparator(path);
+    run("Stack to Images");
+    for (i = nImages; 0 < i; i--) {
+        fileName = getTitle();
+        fileTag = substring(fileName, 0, lastIndexOf(fileName, "-"));
+        fileOut = path + "S" + i + "_" + fileTag + ".tif";
+        saveAs("Tiff", fileOut);
+        close();
+    }
+}
+
 
 /* get all files from direcotry
   * @param: output directory
   * @param: list of files
   */
- function preprocessStacks(path, files)
+function preprocessStacks(path, files)
 {
-    path = checkPathSeparator(path);
     for(f = 0; f < files.length; f++) {
         showProgress(f, files.length);
         fileIn = files[f];
         fileName = File.getName(fileIn);
-        fileTag = substring(fileName, 0, lastIndexOf(fileName, "."));
-        fileOut = path + fileName;
+        
         run("Bio-Formats Windowless Importer", "open="+fileIn);
-
-        getMinAndMax(min, max);
-        setMinAndMax(0, max - min);
-        print("min: " + min);
-        print("max: " + max);
-
-        getMinAndMax(min, max);
-        print("new min: " + min);
-        print("new max: " + max);
-
-        //run("Stack to Images");
-        //selectWindow(fileTag + "-0002");
-        //saveAs("Tiff", fileOut);
-        //close();
-        //closeImageByTitle(fileTag + "-0001");
-        break;
+        convertSignedToUnsigned16bit();
+        exportStackToImages(path);
+        //break;
     }
-
-
 }
 
 macro "ScanImageStitching"
@@ -99,7 +122,7 @@ macro "ScanImageStitching"
     filesList = getFileListWithExtension(pathInput, ".tif");
 
     // pre-process
-    setBatchMode(false);
+    setBatchMode(true);
     preprocessStacks(pathTemp, filesList);
     setBatchMode(false);