Beginner's Help: Counting particles across several images

I work for a wildlife conservation charity in the UK, and we want to try and use our drone to count our gull nesting colony in the summer. These are white birds on a dark background, so it was pretty easy on my test photo to work out how to conduct particle analysis to count the total birds.

However, our plan is to take identical photographs on several different days across the incubation period, and only count birds that are in the exact same location on each picture - suggesting that they are sitting on eggs, rather than just resting temporarily. Our current manual counts suggest around 4,000 nests.

Is there an existing plug-in that can count the same (white, >15px) features at the same locations across several images, or do we need to create a macro for this?

All help is massively appreciated - none of us have any real programming experience though!

One way to do is to create a composite selection from all 4000 nests.

https://imagej.nih.gov/ij/docs/guide/146-10.html

Threshold the images nests in the first step (or use some advanced classifiers if necessary) and then apply:

Edit->Selection->Create Selection to create a composite selection.

Add the selection to the ROI Manager for a later use (split, extend the single nests with a buffer zone, save the composite ROI, etc.):

https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager

You can now import you time based images e.g. as a image stack (or virtual stack to save memory):

https://imagej.nih.gov/ij/docs/guide/146-26.html#toc-Subsection-26.6

Now threshold the seagulls, enable the composite selection again (click on the ROI in the ROI Manager) and then employ a Particle Analysis on the whole stack to measure only particles (seagulls) in the composite ROI (nests):

https://imagej.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.2

Composite selections can also be created manually by holding the SHIFT key to combine several selections:

https://imagej.nih.gov/ij/docs/guide/146-10.html

Here a screenshot with a stack (imagine a landscape) simulating your nesting locations (yellow composite selection) and the seagulls (thresholded):

And here the result showing that only those particles are measured inside the composite selection:

All images in the stack will be measured. Have also a look to at the Set Measurements dialog to record the stack positions, etc.:

https://imagej.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.7

Many thanks for the response! I will give it a try and see if it is what we are after.

This is really great, is does give me a count and location of particles for each slice, but can it give me a count of white points visible at the same location across the stack?

Just threshold the white points or any other are (the points you see in the example are thresholded=red)

Thank you for taking the time to explain all this! We’re just trying it now and it works brilliantly!