Deep learning (DL) is a powerful tool to extract ecological information from large image datasets efficiently and consistently. However, applying these methods remains challenging, due in part to the complexity of DL workflows and the dynamic nature of available tools. To address this, we created a practical guide and review, focused on one of the fundamental tasks in automated image analysis: image classification. Our approach integrates commonly used software and highlights key steps-from image acquisition to annotated, model-ready datasets, to training, evaluation and deployment. It is modular and supported by a flexible code base (in Python, with R alternatives where possible) and Graphical User Interfaces (GUIs), enabling adaptation to different models and ecological objectives. The goal is to empower ecologists to confidently incorporate computer vision into their research. We illustrate this approach, using an open-source ROV dataset from the Norwegian Sea, featuring deep-sea biotopes defined by multivariate clusters of depth, substrate type, and associated species. To balance accessibility for users alongside performance, we focused on CNN models from the Ultralytics ML Platform (YOLO V.8 and V.11), comparing the full suite of architectures that range in complexity and efficiency. Cross-validation revealed high overall performances and that larger, more complex models are not always superior, with YOLO V.8m best (accuracy and macro-averaged performance metrics = ~0.97-0.98). Notably, high performances were achieved despite labels being based on both visual and external environmental predictors, suggesting visual features alone were sufficient for classification in this dataset. We highlight that the decision to deploy a model must be made in light of the study's objectives, with domain-based reasoning and experience guiding every stage of implementation. This work offers a practical blueprint for implementing DL in ecological research, promoting broader adoption and supporting reproducibility and more efficient, standardised, and sustainable monitoring; in this case of deep-sea biotopes, which is essential for marine spatial planning.
