How to do Image Thresholding in ImageJ


Hi today, I will demonstrate image thresholding using imageJ Let’s open an image in this image, these bright stuffs are islands of gold nanoparticles seen under optical microscope I want to know the area of each these individual islands so, before knowing the area I need to threshold this image and then I will measure the area of each island notice here, this image is a color image RGB also indicates red, green, and blue so for the measurement, we need to convert this into black & white image before converting into black & white image let’s calibrate this image analyze set scale 1024 pixels equal to 175 µm now, our image is calibrated and let’s duplicate it ok, now this number 1 image is our duplicated so, we need to convert this image into black & white image so go into image type 8-bit this is our black & white image now, we have to threshold this image image type sorry, adjust threshold notice here, while thresholding some of the part is okay but this part, top part of the image is completely washed away this is very bad very bad so, we don’t want this if, we slightly change the intensities in the histogram the lower part of the our image gets washed away and we totally lose the information in our image so, this is not a good way to threshold threshold our image so, there are two ways still we can deal this deal with this image the one way is we can select the part of the image like this part then basically we can duplicate the selected part so, this part we can threshold very nicely you can see here image adjust threshold which is a very nice but if we want to do threshold entire image then we have to use filter although there are other ways so, in this video I will show using filter how we can threshold sorry, how we can maintain the uniform background throughout the image let’s reset this image let’s go into process FFT bandpass filter let’s apply this filter notice here our islands are strikingly bright while the background is very dark now, the thresholding would be very easy let’s apply the thresholding image adjust threshold so, you can see our thresholding is very nice almost no loss of information so, let’s see over and under you can play with the histogram and you can determine to what extent you can move the the buttons to determine the right threshold in this case, the auto option seems working very nicely so, let’s apply this one so, our this image is now thresholded now, we can analyze and let’s measure the area let’s check the area option now, let’s go in analyze analyze particles let’s put the lower limit around 5 notice here, choose this overlay outlines to check whether our thresholding was done properly or not and don’t forget to click here add to manager option okay now the area is calculated for each island and that is displayed here the island no. 1 has an area of 7.856 µm² so but our purpose is to check whether our thresholding is correct or no let’s close this image or, let’s minimize this image let’s choose the original image you can see this is an area 1 particle 1, 2, 3, 4 the yellow line looks very well fitted around the particles or islands so that means our our thresholding was done properly so the another thing in this one is we can also label the islands with different color so that we can identify easily For example, let’s this island no. 30 and we can label it as a red so the islands becomes red which we can see and you can choose another island and you can make another island blue if you like so, let’s click on show all option so, you can see, we label this island as a red this is a blue so, this is sometimes very helpful to identify the desired island from the rest of the islands Hope this helps Thank you for watching

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4 thoughts on “How to do Image Thresholding in ImageJ

  1. I am a researcher at University of Maine and this was very helpful to teach me threshold when binary does not work. Thank you very much!!!

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