DOI: 10.5281/zenodo.7849417
title: replicAnt - Plum2023 - Detection & Tracking Datasets and Trained Networks

description: This dataset contains all recorded and hand-annotated as well as all synthetically generated data as well as representative trained networks used for detection and tracking experiments in the<em> replicAnt - generating annotated images of animals in complex environments using Unreal Engine</em> 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. <strong>Abstract:</strong> 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. <strong>Benchmark data</strong> Two video datasets were curated to quantify detection performance; one in laboratory and one in field conditions. The laboratory dataset consists of top-down recordings of foraging trails of <em>Atta vollenweideri</em> (Forel 1893) leaf-cutter ants. The colony was collected in Uruguay in 2014, and housed in a climate chamber at 25°C and 60% humidity. A recording box was built from clear acrylic, and placed between the colony nest and a box external to the climate chamber, which functioned as feeding site. Bramble leaves were placed in the feeding area prior to each recording session, and ants had access to the recording area at will. The recorded area was 104 mm wide and 200 mm long. An OAK-D camera (OpenCV AI Kit: OAK-D, Luxonis Holding Corporation) was positioned centrally 195 mm above the ground. While keeping the camera position constant, lighting, exposure, and background conditions were varied to create recordings with variable appearance: The “base” case is an evenly lit and well exposed scene with scattered leaf fragments on an otherwise plain white backdrop. A “bright” and “dark” case are characterised by systematic over- or underexposure, respectively, which introduces motion blur, colour-clipped appendages, and extensive flickering and compression artefacts. In a separate well exposed recording, the clear acrylic backdrop was substituted with a printout of a highly textured forest ground to create a “noisy” case. Last, we decreased the camera distance to 100 mm at constant focal distance, effectively doubling the magnification, and yielding a “close” case, distinguished by out-of-focus workers. All recordings were captured at 25 frames per second (fps).<br> <br> The field datasets consists of video recordings of <em>Gnathamitermes</em> sp. desert termites, filmed close to the nest entrance in the desert of Maricopa County, Arizona, using a Nikon D850 and a Nikkor 18-105 mm lens on a tripod at camera distances between 20 cm to 40 cm. All video recordings were well exposed, and captured at 23.976 fps.<br> <br> Each video was trimmed to the first 1000 frames, and contains between 36 and 103 individuals. In total, 5000 and 1000 frames were hand-annotated for the laboratory- and field-dataset, respectively: each visible individual was assigned a constant size bounding box, with a centre coinciding approximately with the geometric centre of the thorax in top-down view. The size of the bounding boxes was chosen such that they were large enough to completely enclose the largest individuals, and was automatically adjusted near the image borders. A custom-written Blender Add-on aided hand-annotation: the Add-on is a semi-automated multi animal tracker, which leverages blender’s internal contrast-based motion tracker, but also include track refinement options, and CSV export functionality. Comprehensive documentation of this tool and Jupyter notebooks for track visualisation and benchmarking is provided on the <em>replicAnt</em> and BlenderMotionExport GitHub repositories. <strong>Synthetic data generation</strong> Two synthetic datasets, each with a population size of 100, were generated from 3D models of \textit{Atta vollenweideri} leaf-cutter ants. All 3D models were created with the <em>scAnt</em> photogrammetry workflow. A “group” population was based on three distinct 3D models of an ant minor (1.1 mg), a media (9.8 mg), and a major (50.1 mg) (see 10.5281/zenodo.7849059)). To approximately simulate the size distribution of <em>A. vollenweideri </em>colonies, these models make up 20%, 60%, and 20% of the simulated population, respectively. A 33% within-class scale variation, with default hue, contrast, and brightness subject material variation, was used. A “single” population was generated using the major model only, with 90% scale variation, but equal material variation settings.<br> <br> A <em>Gnathamitermes</em> sp. synthetic dataset was generated from two hand-sculpted models; a worker and a soldier made up 80% and 20% of the simulated population of 100 individuals, respectively with default hue, contrast, and brightness subject material variation. Both 3D models were created in Blender v3.1, using reference photographs.<br> <br> Each of the three synthetic datasets contains 10,000 images, rendered at a resolution of 1024 by 1024 px, using the default generator settings as documented in the Generator_example level file (see documentation on GitHub). To assess how the training dataset size affects performance, we trained networks on 100 (“small”), 1,000 (“medium”), and 10,000 (“large”) subsets of the “group” dataset. Generating 10,000 samples at the specified resolution took approximately 10 hours per dataset on a consumer-grade laptop (6 Core 4 GHz CPU, 16 GB RAM, RTX 2070 Super). <br> Additionally, five datasets which contain both real and synthetic images were curated. These “mixed” datasets combine image samples from the synthetic “group” dataset with image samples from the real “base” case. The ratio between real and synthetic images across the five datasets varied between 10/1 to 1/100. <strong>Funding</strong> 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.