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I have recently started volunteering at a lab and have been given this open-ended ended task. I have never done any digital image analysis before which is why I come here for assistance. In this case I have been given an image of certain cells stained with oil red O (the image contains a black background and blobs of oil red O stained lipid droplets). My supervisor already has a process to measure the area of each lipid droplet in an image (using ImageJ), and then sort the data into bins. This is to display the frequency of increasing sizes of lipid droplets under different conditions.

Now, I have been given the images of interest and corresponding excel files which contains 2 columns. The first column simply numbers the lipid droplet (lets say 1-255) and the second column contains the size of each lipid droplet in pixels. Just using these 2 pieces of information I now have to to develop a method to colour code the different sized lipid droplets in each cell. So lets say the lipid droplets between the sizes of 50-500 pixels would be yellow and 500-1000 pixels would be red, etc. Could someone tell me how to do this task? I am not even sure what software to use (but my supervisor mentioned that I can try using ImageJ, R and even Python). Any help will be appreciated, thanks.

I tried using imageJ but I am having major troubles. Since the images and the associated excel files contain are completely seperate, would it even be possible for me to use the given excel files for the colouring process in any way? How would ImageJ (or any other software) match up the given area of a droplet in the excel file to the corresponding droplet in an image? The only way I could possibly think of is remeasuring the area of the droplets of each entry in the excel file and also recording the the X and Y coordinates for the center of each droplet. I am completely lost at this point to be honest.

dantebuppi12
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  • Welcome to SO dantebuppi12. Stackoverflow is generally for coding and programming issues rather than advice regarding software. Having said that, you could update your question with some example data e.g. one image with its corresponding table and this might improve your chances of receiving a meaningful answer. Thanks, and good luck. – L Tyrone May 12 '23 at 02:20
  • from your description it does seem like this might be easier when done upstream of your current point, but there's something important missing here - what's your desired output? If it's just "colour code these based on ranges" then excel's conditional formatting will have the job done in seconds. If you actually want to produce colour-adjusted versions of the images then it's a different task altogether. Can you ask your supervisor for a copy of the code they use, so you can tinker without interfering with the existing workflow? – Paul Stafford Allen May 12 '23 at 08:15
  • @PaulStaffordAllen Based on my understanding, I need to colour-code the image itself based on ranges (of area). Also, my supervisor used ImageJ to produce the area data for the lipid droplets, so I don't think there is any associated code. – dantebuppi12 May 15 '23 at 01:42

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