how to remove speckle type noise in an image using threshold intensity

all

i have an image that i want to use intensity threshold to find spots which have a stain ( darker parts). the problem is that my image has lots of speckles and when i use this method it also picks up some of the speckles too.in the attached image (picture 2) i show which stains im interested to detect but it sometimes goes and detect speckles too (picture 3)

Answer 1

[Image Analyst]

Can you average several images together to reduce the noise? Otherwise you might just have to manually trace them because even I can't decide why you circled only those images and no other regions that look similar. Is anything fixed pattern noise? If so you might be able to detect that, like by taking an image with the lens removed, or taking a picture with no sample in place (just the background illumination).

[Akram]

thanks very much for the comment. I should have used a better image. i have attached a new image here

picture 4. thats what i want to identify ( red circles) but if i only choose a threshold based on like 4 % intensity drop it will grab so many other things/features in the image as well ( picture 5). I am using a 3*3 convolution filter. i can increase it to 9*9 pixel and change the intensity threshold to something larger, but then sometimes it doesnt detect the actual particles im interested to catch.