Threshold each image in the sequence with a threshold that makes the LED:s visible. If you can threshold it with a threshold that only keeps the LED and removes background then you are more or less finished since all you need to do now is to keep track of each position that has seen a LED and count how often it occurs.
As a middle step, if there is "background noise" in the thresholded image would be to use erosion to remove small mistakes, and then maybe dilate to "close holes" in the blobs you are actually interested in.
If the scene is static you could also make a simple background model by taking the median of a few frames and removing the resulting median image from any frame and threshold that. Stuff that has changed (your LEDs) will appear stronger.
If the scene is moving I see no other (easy) solution than making sure the LED are bright enough to be able to use the threshold approach given above.
As for OpenCV: if you know what you want to do, it is not very hard to find a function that does it. The hard part is coming up with a method to solve the problem, not the actual coding.
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