See my ImageJ protocols for quantifying lipid droplets for inspriation. Set a scale for the image and then report the area of each star. As discussed above, the threshold may need to be changed. For example, try counting cell nuclei that have been stained with DAPI. Test the star counting macro on images of other objects to be counted. Note that using different thresholds on images in a set can alter count results controlling for camera settings and time/location in batches of images is the best way to avoid threshold bias. Consider chaning the threshold to the one that works best for your images. Therefore, pictures taken with differet settings or at different times/locations often require different thresholds. Thresholding takes the overall brightness and contrast of an image into account. You’ll find the problem by examining the saved thresholded images: thresholding is failing. On your own star images, you may notice that the stars aren’t counted properly. This type of error can be dealt with by adding a watershed step (LINK TO PAGE). On the accuracy front, you may have noticed that there is a mistake made on “StarsToCount2.jpg”: two stars appear so close together that they are counted as one. Thresholded images will appear in the folder selected.Įdit the contents of “CountStarsInFolder.ijm” to improve the accuracy of counting, or completely rework the contents to perform your own image quantification tasks. Star counts will appear in the Summary window (9, 32, and 19 stars in images 1, 2, and 3, respectively). Do not make a new folder inside the folder from step 7. Select a different folder in which thresholded images will be placed. Select the folder in which your images are stored.
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