I3S Pattern

We would like to state that we have no commercial or scientific interests. All we want is to help the community to improve research and in this way help conservation of endangered species. We do this (in our spare time) simply because we enjoy it and want to contribute.

All work is done for free, but as owners of small enterprises, working on the tool also means no income whatsoever. Donations or grants for future development are most welcome.


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Introduction to I3S Pattern

I3S Pattern is the tool for species with hard to annotate markings. This may mean markings which cannot be annotated using spot centers or ellipses. Pattern may also be suitable for species with lots of small spots making it difficult to choose about 30 spots consistently. Pattern only requires you to identify the three reference points, and the general identification area. After this, the relevant key points are extracted automatically. Each key point has a size and location, denoted by a circle with varying diameter.

Please consider the fact that automatic key point extraction provides ease of use but also comes at a price. The price being the fact that key point extraction is susceptible to flash highlights, murky water, etc. When annotating everything manually, as is the case with I3S Classic and Spot (Manta) and even with Contour, you can correct for difficult visual conditions. This is much less possible with Pattern. You can try to exclude these areas when indicating the identification area, but only to a limited extent. Therefore, automatic key point extraction will not be better than the human visual system!

When you start using I3S Pattern for a new species it might be necessary to change some internal parameters. These parameters are identified in the file “metadata.xml” to be found in the database directory. The most prominent parameter is the number of key points (nrElements) in the area. This number is by default 35, optimized for turtles. Because of the large visual variation in turtle heads, it is expected that turtles are at the high end of key point numbers. In other words, it is not expected that for many species increasing the number of key points will increase accuracy. In fact, it may even decrease accuracy while it certainly increases search time.

So, for many species a lower number may be required. The optimal number is determined by the size of the area and the visual variation in this area. If there is not much variation, a lower number is more appropriate. Remember, the software will always find the number of requested key points, and if there is not much variation, a significant part of the key points may not be meaningful if the key point number is too high. The optimal setting is best determined with an experiment with 30-40 individuals and 2-3 photos per individual.

If you want advice in the setting of the number of key points and other internal parameters you are referred to the Pattern manual coming with the installation. You can also contact us directly via e-mail.