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--- post:meanintinellipse.m [2019/10/11 14:40] – pseudomoaner
+++ post:meanintinellipse.m [2019/11/18 16:45] (current) – pseudomoaner
@@ Line 1: / Line 1: @@
 ====== meanIntInEllipse.m =====
+**Class:** Function
 **Description:** Takes in a specified element of the [[usage:tracking#outputs|procTracks]] data structure and an image, and calculates the average intensity of pixels in that image within an ellipse with geometry defined by the selected object.
@@ Line 29: / Line 31: @@
 %Rescale ellipse parameters
-xPx = procTrack.x(ind)/pxSize;
+xPx = round(procTrack.x(ind)/pxSize);
-yPx = procTrack.y(ind)/pxSize;
+yPx = round(procTrack.y(ind)/pxSize);
-minLenPx = procTrack.minorLen(ind)*2/pxSize;
+minLenPx = round(procTrack.minorLen(ind)/pxSize);
-majLenPx = procTrack.majorLen(ind)*2/pxSize;
+majLenPx = round(procTrack.majorLen(ind)/pxSize);
 phi = procTrack.phi(ind);
@@ Line 62: / Line 64: @@
 </code>
+**Example usage**
+<code matlab>
+  imgLoc = 'FluoImg.tif';
+  trackLoc = 'Tracks.mat';
+  load(trackLoc,'procTracks')
+  %Get the pixel size from the input image
+  imgInfo = imfinfo(imgLoc);
+  pixelSize = 1/imgInfo.XResolution;
+  %Load the image
+  imPlane = double(imread(startImgLoc,'Index',1));
+  %Get the mean and total fluorescence of the object in track 10 at timepoint 1
+  [meanFluo,totalFluo] = meanIntInEllipse(imPlane,procTracks(10),1,pixelSize);
+</code>
+**Example output:** Histogram of mean object intensities for a set of tracks with an associated fluorescence image at their first timepoint. For more details see [[post:labelstartandendfluocells.m]].
+{{ :post:fluosplitexample2.png?nolink&400 |}}