README.md

---
license: cc-by-sa-4.0
---
# Re-created Beetle Elytra Dataset

This dataset is a **re-created** version of the original [2018-NEON-beetles](https://huggingface.co/datasets/imageomics/2018-NEON-beetles) dataset, augmented with:
- **Bounding boxes** for beetle object detection.
- **Manually refined elytra coordinates** for precise morphological measurements.

Our goal is to **streamline automated beetle trait analysis** by providing curated ground truths suitable for training and benchmarking deep learning models.

### What’s Included
- **High-resolution images** featuring multiple beetles, each with a scale bar and barcode.  
- **Bounding box annotations** for each beetle (extracted using contour detection on Segment Anything Model (SAM) masks).  
- **Elytra coordinates** for morphological trait estimation, specifically measuring elytra length and width.

## Dataset Creation Process

1. **Original Dataset**  
   - We started with the [2018-NEON-beetles](https://huggingface.co/datasets/imageomics/2018-NEON-beetles) dataset, which had images and partial morphological annotations provided via [Zooniverse](https://www.zooniverse.org/).
   
2. **Segmentation & Bounding Box Extraction**  
   - We leveraged the [Segment Anything Model (SAM)](https://github.com/facebookresearch/segment-anything) to generate masks for each beetle.  
   - **Contour detection** was applied to masks to produce bounding box coordinates.

3. **Elytra Annotation Recalibration**  
   - The original elytra keypoints from Zooniverse were mapped to the newly cropped bounding boxes.  
   - Adjustments were made to ensure consistent coordinate references (top-left origin, pixel-based).

4. **Final Verification**  
   - A small portion of images were manually inspected to confirm the correctness of bounding boxes and elytra points.  
   - Any outliers or flawed annotations were corrected.

## Intended Uses

- **Object Detection**: Training and evaluating models (e.g., YOLO) to detect and localize beetles in group images.  
- **Coordinate Regression**: Predicting elytra keypoints for morphological trait analysis (length, width).  
- **Ecological/Biodiversity Research**: Enabling large-scale measurement and comparison across beetle populations.

## Citation
### BibTeX:
```
@inproceedings{Yoo2025EfficientCNN,
  author    = {Yoo, H. and Somasundaram, D. and Oh, H.},
  title     = {{Efficient CNN-Based System for Automated Beetle Elytra Coordinates Prediction}},
  booktitle = {Proceedings of the 20th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications ({VISIGRAPP} 2025) - Volume 2: {VISAPP}},
  pages     = {934--941},
  year      = {2025},
  publisher = {{SCITEPRESS – Science and Technology Publications, Lda.}},
  doi       = {10.5220/0013264600003912},
  isbn      = {978-989-758-728-3},
  issn      = {2184-4321},
  series    = {{VISIGRAPP} 2025}
}
```

### Original Dataset:
```
@misc{Fluck2018_NEON_Beetle,
  author = {Isadora E. Fluck and Benjamin Baiser and Riley Wolcheski and Isha Chinniah and Sydne Record},
  title = {2018 {NEON} Ethanol-preserved Ground Beetles (Revision 7b3731d)},
  year = {2024},
  url = {https://huggingface.co/datasets/imageomics/2018-NEON-beetles},
  doi = { 10.57967/hf/5252 },
  publisher = {Hugging Face}
}
```

### Specimens:
```bibtex
@misc{Portal2022-ho,
  title     = "{NEON} biorepository Carabid collection (trap sorting)",
  author    = "Portal, Neon Biorepository",
  abstract  = "This collection contains subsamples of Carabid adults from pitfall sampling from a single trap (NEON sample class:
               bet\_sorting\_in.subsampleID.bet). Ground beetles are sampled using pitfall traps (16 oz deli containers filled with 150 or
               250 mL of propylene glycol). Four (pre-2018) or 3 (2018 and beyond) traps are deployed in each of 10 (pre-2023) or 6 (2023
               and beyond) plots at each terrestrial NEON site, with traps arrayed approximately 20 meters from the center of the plot.
               Sampling occurs biweekly throughout the growing season (when temperatures are above 4 degrees C). Following trap collection,
               all beetles from the family Carabidae are sorted by NEON technicians and identified to species or morphospecies. A subset
               of collected Carabidae are pointed or pinned, while other specimens (non-pinned/non-pointed carabids, invertebrate
               bycatch, and vertebrate bycatch) are stored in 95\% ethanol for archiving. Regardless of storage method, all collections data
               are reported at a per trap resolution. A subset of pinned ground beetles (up to 467 per site per year) are sent to an expert
               taxonomist for secondary identification. Identifications performed on these individuals may be used to estimate
               uncertainty in parataxonomist identification by NEON technicians.",
  publisher = "National Ecological Observatory Network",
  doi = {https://doi.org/10.15468/mjtykf},
  note = {Accessed in 2022}
}
```

```bibtex
@misc{Portal2022-qu,
  title     = "{NEON} Biorepository Carabid Collection (Archive Pooling)",
  author    = "Portal, Neon Biorepository",
  abstract  = "This collection contains subsamples of Carabid adults from pitfall sampling and pooled across multiple traps within a plot
               (NEON sample class: bet\_archivepooling\_in.subsampleID.bet). Ground beetles are sampled using pitfall traps (16 oz deli
               containers filled with 150 or 250 mL of propylene glycol). Four (pre-2018) or 3 (2018 and beyond) traps are deployed in each of
               10 (pre-2023) or 6 (2023 and beyond) plots at each terrestrial NEON site, with traps arrayed approximately 20 meters from the
               center of the plot. Sampling occurs biweekly throughout the growing season (when temperatures are above 4 degrees C).
               Following trap collection, all beetles from the family Carabidae are sorted by NEON technicians and identified to species or
               morphospecies. A subset of collected Carabidae are pointed or pinned, while other specimens (non-pinned/non-pointed carabids,
               invertebrate bycatch, and vertebrate bycatch) are stored in 95\% ethanol for archiving. A subset of pinned ground beetles (up to
               467 per site per year) are sent to an expert taxonomist for secondary identification. Identifications performed on these
               individuals may be used to estimate uncertainty in parataxonomist identification by NEON technicians.",
  publisher = "National Ecological Observatory Network",
  doi = {https://doi.org/10.15468/xicbza},
  note = {Accessed in 2022}
}
```

## Acknowledgements
This work was supported by the NSF OAC 2118240 Imageomics Institute award and was initiated at Beetlepalooza 2024. More details about Beetlepalooza can be found on https://github.com/Imageomics/BeetlePalooza-2024.

This material is based in part upon work supported by the [U.S. National Ecological Observatory Network (NEON)](https://www.neonscience.org/), a program sponsored by the [U.S. National Science Foundation (NSF)](https://www.nsf.gov/) and operated under cooperative agreement by [Battelle](https://www.battelle.org/). Furthermore, this material uses specimens and/or samples collected as part of the NEON Program.