replicAnt - Plum2023 - Segmentation Datasets and Trained Models

This dataset contains all recorded and hand-annotated as well as all synthetically generated data as well as representative trained networks used for semantic and instance segmentation experiments in the replicAnt - generating annotated images of animals in complex environments using Unreal Engine manuscript. Unless stated otherwise, all 3D animal models used in the synthetically generated data have been generated with the open-source photgrammetry platform scAnt peerj.com/articles/11155/.  All synthetic data has been generated with the associated replicAnt project available from https://github.com/evo-biomech/replicAnt.

Abstract:

Deep learning-based computer vision methods are transforming animal behavioural research. Transfer learning has enabled work in non-model species, but still requires hand-annotation of example footage, and is only performant in well-defined conditions. To overcome these limitations, we created replicAnt, a configurable pipeline implemented in Unreal Engine 5 and Python, designed to generate large and variable training datasets on consumer-grade hardware instead. replicAnt places 3D animal models into complex, procedurally generated environments, from which automatically annotated images can be exported. We demonstrate that synthetic data generated with replicAnt can significantly reduce the hand-annotation required to achieve benchmark performance in common applications such as animal detection, tracking, pose-estimation, and semantic segmentation; and that it increases the subject-specificity and domain-invariance of the trained networks, so conferring robustness. In some applications, replicAnt may even remove the need for hand-annotation altogether. It thus represents a significant step towards porting deep learning-based computer vision tools to the field.

Benchmark data

Semantic and instance segmentation is used only rarely in non-human animals, partially due to the laborious process of curating sufficiently large annotated datasets. replicAnt can produce pixel-perfect segmentation maps with minimal manual effort. In order to assess the quality of the segmentations inferred by networks trained with these maps, semi-quantitative verification was conducted using a set of macro-photographs of Leptoglossus zonatus (Dallas, 1852) and Leptoglossus phyllopus (Linnaeus, 1767), provided by Prof. Christine Miller (University of Florida), and Royal Tyler (Bugwood.org. For further qualitative assessment of instance segmentation, we used laboratory footage, and field photographs of Atta vollenweideri provided by Prof. Flavio Roces. More extensive quantitative validation was infeasible, due to the considerable effort involved in hand-annotating larger datasets on a per-pixel basis.

Synthetic data

We generated two synthetic datasets from a single 3D scanned Leptoglossus zonatus (Dallas, 1852) specimen: one using the default pipeline, and one with additional plant assets, spawned by three dedicated scatterers. The plant assets were taken from the Quixel library and include 20 grass and 11 fern and shrub assets. Two dedicated grass scatterers were configured to spawn between 10,000 and 100,000 instances; the fern and shrub scatterer spawned between 500 to 10,000 instances. A total of 10,000 samples were generated for each sub dataset, leading to a combined dataset comprising 20,000 image render and ID passes. The addition of plant assets was necessary, as many of the macro-photographs also contained truncated plant stems or similar fragments, which networks trained on the default data struggled to distinguish from insect body segments. The ability to simply supplement the asset library underlines one of the main strengths of replicAnt: training data can be tailored to specific use cases with minimal effort.

Funding

This study received funding from Imperial College’s President’s PhD Scholarship (to Fabian Plum), and is part of a project that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 851705, to David Labonte). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.