Species identification in camera trap images has been widely studied, but key ecological modeling tasks such as species abundance or density estimation also require counting individual animals. However, the lack of counting labels in most datasets and low frame rates (typically ~1 frame per second) make sequence-level tracking and count estimation particularly challenging. In this work, we present PuTR-CouT, a counting-by-tracking framework built on a transformer-based learned association mechanism for sequence-level animal counting in camera trap images. To address the scarcity of annotated tracking data, we generate synthetic training data by exploiting structural priors, such as static backgrounds and short temporal bursts, to heuristically create pseudo-tracking labels in a weakly supervised manner. The resulting tracker associates detections across frames, using these tracks to estimate per-species counts. We also refine the MaxBoxCount heuristic used by the top solutions of the iWildCam 2021 challenge as a strong baseline, setting the highest score reported to date. When evaluated on the iWildCam 2021 benchmark, our framework PuTR-CouT delivers competitive counting results compared to the improved MaxBoxCount, with the added capability of multi-species predictions and track-level verification.

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