Automatic counting of cones of coniferous species

Hi,
We have a project in which we need to evaluate level of fructification in seed orchards or selected seed stands of coniferous species (here Larix sp.), thus from hundreds of trees. Subjective scoring is often used to do so, but we’d like to improve the evaluation through automatic counting of cones. So we have taken hundreds of cell phone pictures of trees such as in the above picture. I understand that jpeg format is not recommended.
As you see cones might be intermixed with branches and share a similar brownish colour with the trunk and branches. Part are located in the upper tree with a sky background, part in the lower part with a ground background.
Would there be a way to isolate cones from other organs so to easily and automatically count them?
I am able to manually count them for example with cell counter but my expertise with Image J is really basic.
Thanks,