This might be helpful https://www.researchgate.net/post/How_can_I_get_the_temperature_at_each_pixel_of_the_IR_image_taken_by_FLIR_T250_camera

This might be helpful https://www.researchgate.net/post/How_can_I_get_the_temperature_at_each_pixel_of_the_IR_image_taken_by_FLIR_T250_camera

If you're using FLIR this may help you https://cran.r-project.org/web/packages/Thermimage/Thermimage.pdf.

A built-in toolbox in Matlab could be useful for thermal image analysis.

Check out this example: https://www.mathworks.com/company/newsletters/articles/automating-image-registration-with-matlab.html

and a video webinar on how to perform thermal analysis can be viewed here: https://www.mathworks.com/videos/thermal-analysis-with-matlab-and-flir-cameras-98177.html?elqsid=1514345343105&potential_use=Education

Thank you all for the help! To be more specific, the main challenge is to be able to isolate the plants in an IR image and quantify their temperature. In most of the IR software this can be done by setting the temperature threshold in a way to exclude the background temperatures. In my case this cannot be done because the temperature of the plants may sometimes be equal to that of the background. One possible solution is to subtract plant temperature via the help of an identical VIS image. In other words, the VIS image can be used to select the pixels corresponding to plants and then apply this information to the IR image. Does somebody know the steps to do that using a freeware like imagej?

Here is link on how to subtract 2 images using ImageJ: http://imagej.1557.x6.nabble.com/Subtracting-one-image-from-another-td5005838.html

Or if you are using Matlab, you can use the imsubtract function: https://ch.mathworks.com/help/images/ref/imsubtract.html

Thanks Omar!!! That helped a bit! I think i am in the proper way now!