Add requirements files, citation file, and reference to Funcapalooza

.github/workflows/validate-zenodo.yaml

@@ -0,0 +1,23 @@
+name: Check zenodo metadata
+
+on:
+    push:
+        paths:
+          - '.zenodo.json'
+          - '.github/workflows/validate-zenodo.yaml'
+
+jobs:
+  check-zenodo-metadata:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-node@v6
+        with:
+          node-version: '24'
+      - name: Install dependencies
+        run: npm install zenodraft@0.14.1
+      - name: Check .zenodo.json file
+        run: |
+          npx zenodraft metadata validate .zenodo.json 

.zenodo.json

@@ -0,0 +1,127 @@
+{
+  "creators": [
+    {
+      "name": "Liu, Fangxun",
+      "affiliation": "The Ohio State University",
+      "orcid": "0009-0008-8508-2776"
+    },
+    {
+      "name": "Rayeed, S M",
+      "affiliation": "Rensselaer Polytechnic Institute"
+    },
+    {
+      "name": "Stevens, Samuel",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "East, Alyson",
+      "affiliation": "The University of Maine"
+    },
+    {
+      "name": "Chiang, Cheng Hsuan",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Lee, Colin",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Yi, Daniel",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Yang, Junke",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Naik, Tejas",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Wang, Ziyi",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Kilrain, Connor",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Buckwalter, Elijah H.",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Hou, Jiacheng",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Bueno, Saul Ibaven",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Wang, Shuheng",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Ma, Xinyue",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Liu, Yifan",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Tao, Zhiyuan",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Zhang, Ziheng",
+      "affiliation": "The Ohio State University"
+    },
+    {
+      "name": "Sokol, Eric",
+      "affiliation": "National Ecological Observatory Network (NEON), Battelle"
+    },
+    {
+      "name": "Belitz, Michael",
+      "affiliation": "Michigan State University"
+    },
+    {
+      "name": "Record, Sydne",
+      "affiliation": "The University of Maine"
+    },
+    {
+      "name": "Stewart, Charles V.",
+      "affiliation": "Rensselaer Polytechnic Institute"
+    },
+    {
+      "name": "Chao, Wei-Lun",
+      "affiliation": "The Ohio State University"
+    }
+  ],
+  "description": "Pipeline for processing large-scale tray images of pinned beetles: detect specimens, optionally sort and crop with metadata matching, and produce fine-grained morphological segmentation (5-class or 9-class). It uses an open-vocabulary detector (Grounding DINO), a vision-language model (LLaVA-NeXT) for verification, and fine-tuned Mask2Former for transformer-based part segmentation and downstream morphological analysis.",
+  "keywords": [
+    "deep learning",
+    "computer vision",
+    "image processing",
+    "object detection",
+    "image segmentation",
+    "entomology",
+    "imageomics"
+  ],
+  "license": {
+    "id": "MIT"
+  },
+  "publication_date": "2026-07-07",
+  "title": "BeetleFlow: An Integrative Deep Learning Pipeline for Beetle Image Processing",
+  "version": "1.0.0",
+  "grants": [
+    {
+      "id": "021nxhr62::2118240"
+    }
+  ],
+  "references": [
+    "East, A., Belitz, M., Cotton, L., Dominguez, J., Betancourt, I., Rayeed, S. M., Liu, F., Carlyn, D., Kilrain, C., Wu, J., Earl, C., Lapp, H., Perry, K. I., Stewart, C., Thompson, M. J., Campolongo, E. G., Chao, W.-L., Sokol, E. R., & Record, S. (2026). Beetles as Sentinel Taxa: Predicting drought conditions from NEON specimen imagery (Revision 5026be7). Hugging Face. https://doi.org/10.57967/hf/8716",
+    "National Ecological Observatory Network. (2025). Ground beetles sampled from pitfall traps (DP1.10022.001). https://doi.org/10.48443/CD21-Q875",
+    "National Ecological Observatory Network. (2025). NEON Field Site Metadata. Retrieved June 25, 2025, from https://www.neonscience.org/field-sites/exports/NEON_Field_Site_Metadata_20250625"
+  ]
+}

CITATION.cff

@@ -0,0 +1,145 @@
+cff-version: 1.2.0
+message: "If you find this software helpful in your research, please cite both the software and our paper."
+
+title: "BeetleFlow: An Integrative Deep Learning Pipeline for Beetle Image Processing"
+abstract: >-
+  Pipeline for processing large-scale tray images of pinned beetles: detect specimens,
+  optionally sort and crop with metadata matching, and produce fine-grained morphological
+  segmentation (5-class or 9-class). It uses an open-vocabulary detector (Grounding DINO),
+  a vision-language model (LLaVA-NeXT) for verification, and fine-tuned Mask2Former
+  for transformer-based part segmentation and downstream morphological analysis.
+
+type: software
+repository-code: "https://github.com/Imageomics/BeetleFlow"
+license: MIT
+
+date-released: 2026-07-07
+version: 1.0.0
+identifiers:
+  - description: "The GitHub release URL of tag 1.0.0."
+    type: url
+    value: "https://github.com/Imageomics/BeetleFlow/releases/tag/1.0.0"
+
+authors:
+  - family-names: Liu
+    given-names: Fangxun
+    orcid: "https://orcid.org/0009-0008-8508-2776"
+  - family-names: Rayeed
+    given-names: "S M"
+  - family-names: Stevens
+    given-names: Samuel
+  - family-names: East
+    given-names: Alyson
+  - family-names: Chiang
+    given-names: "Cheng Hsuan"
+  - family-names: Lee
+    given-names: Colin
+  - family-names: Yi
+    given-names: Daniel
+  - family-names: Yang
+    given-names: Junke
+  - family-names: Naik
+    given-names: Tejas
+  - family-names: Wang
+    given-names: Ziyi
+  - family-names: Kilrain
+    given-names: Connor
+  - family-names: Buckwalter
+    given-names: "Elijah H."
+  - family-names: Hou
+    given-names: Jiacheng
+  - family-names: Bueno
+    given-names: "Saul Ibaven"
+  - family-names: Wang
+    given-names: Shuheng
+  - family-names: Ma
+    given-names: Xinyue
+  - family-names: Liu
+    given-names: Yifan
+  - family-names: Tao
+    given-names: Zhiyuan
+  - family-names: Zhang
+    given-names: Ziheng
+  - family-names: Sokol
+    given-names: Eric
+  - family-names: Belitz
+    given-names: Michael
+  - family-names: Record
+    given-names: Sydne
+  - family-names: Stewart
+    given-names: "Charles V."
+  - family-names: Chao
+    given-names: "Wei-Lun"
+
+keywords:
+  - deep learning
+  - computer vision
+  - image processing
+  - object detection
+  - image segmentation
+  - entomology
+  - imageomics
+
+preferred-citation:
+  type: conference-paper
+  title: "BeetleFlow: An Integrative Deep Learning Pipeline for Beetle Image Processing"
+  authors:
+    - family-names: Liu
+      given-names: Fangxun
+      orcid: "https://orcid.org/0009-0008-8508-2776"
+    - family-names: Rayeed
+      given-names: "S M"
+    - family-names: Stevens
+      given-names: Samuel
+    - family-names: East
+      given-names: Alyson
+    - family-names: Chiang
+      given-names: "Cheng Hsuan"
+    - family-names: Lee
+      given-names: Colin
+    - family-names: Yi
+      given-names: Daniel
+    - family-names: Yang
+      given-names: Junke
+    - family-names: Naik
+      given-names: Tejas
+    - family-names: Wang
+      given-names: Ziyi
+    - family-names: Kilrain
+      given-names: Connor
+    - family-names: Buckwalter
+      given-names: "Elijah H."
+    - family-names: Hou
+      given-names: Jiacheng
+    - family-names: Bueno
+      given-names: "Saul Ibaven"
+    - family-names: Wang
+      given-names: Shuheng
+    - family-names: Ma
+      given-names: Xinyue
+    - family-names: Liu
+      given-names: Yifan
+    - family-names: Tao
+      given-names: Zhiyuan
+    - family-names: Zhang
+      given-names: Ziheng
+    - family-names: Sokol
+      given-names: Eric
+    - family-names: Belitz
+      given-names: Michael
+    - family-names: Record
+      given-names: Sydne
+    - family-names: Stewart
+      given-names: "Charles V."
+    - family-names: Chao
+      given-names: "Wei-Lun"
+  keywords:
+    - deep learning
+    - computer vision
+    - image processing
+    - object detection
+    - image segmentation
+    - entomology
+    - imageomics
+  collection-title: "NeurIPS 2025 Workshop for Imageomics: Discovering Biological Knowledge from Images Using AI"
+  year: 2025

README.md

@@ -8,7 +8,7 @@
 - [ ] Add installation guide
 
 ## 📊 Dataset
-Beetle part segmentation dataset is available [here](data/) (both 5-class and 9-class).
+Dataset for beetle part segmentation is available [here](data/) (both 5-class and 9-class).
 
 ## 🧑‍💻 Usage
 
@@ -46,6 +46,8 @@ Though the code in this repository is shared under an [MIT License](https://gith
 
 ## Acknowledgments
 
+This work was in part conceived at [Funcapalooza](https://github.com/Imageomics/FuncaPalooza-2025).
+
 This work uses data from the [Beetles as Sentinel Taxa: Predicting drought conditions from NEON specimen imagery dataset](https://huggingface.co/datasets/imageomics/sentinel-beetles). If you make use of the data, please be sure to cite the original source:
 
 BibTeX:
@@ -55,10 +57,10 @@ BibTeX:
     S M Rayeed and Fangxun Liu and David Carlyn and Connor Kilrain and Jiaman Wu and Chandra Earl and Hilmar Lapp 
     and Kayla I. Perry and Charles Stewart and Matthew J. Thompson and Elizabeth G. Campolongo and Wei-Lun Chao and
     Eric R. Sokol and Sydne Record},
-  title = {Beetles as Sentinel Taxa: Predicting drought conditions from {NEON} specimen imagery},
-  year = {2025},
+  title = {Beetles as Sentinel Taxa: Predicting drought conditions from {NEON} specimen imagery (Revision 5026be7)},
+  year = {2026},
   url = {https://huggingface.co/datasets/imageomics/sentinel-beetles},
-  doi = {<doi once generated>},
+  doi = {10.57967/hf/8716},
   publisher = {Hugging Face}
 }
 ```

requirements_detection.txt

@@ -0,0 +1,21 @@
+python>=3.9
+numpy>=1.26
+pandas>=2.2
+torch>=2.4
+torchvision>=0.19
+accelerate>=0.24
+transformers>=4.40.0
+huggingface-hub>=0.34
+tokenizers>=0.21
+safetensors>=0.5
+Pillow>=10.3
+opencv-python>=4.8
+matplotlib>=3.7
+bitsandbytes>=0.43.0
+scipy>=1.11
+tqdm>=4.66
+PyYAML>=6.0
+requests>=2.32
+packaging>=24.1
+typing_extensions>=4.12
+pycocotools>=2.0.7