Imageomics Institute

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108 repositories

bioclip-ecosystem
Public
Centralized resource to describe and link out to all components of the BioCLIP project (Code, Models, Datasets, Spaces).
data code reference
data code reference model benchmarks datasets project-website tree-of-life bioclip
HTML
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MIT License
•0•0•7•1•Updated Mar 5, 2026Mar 5, 2026
Heliconius-model-mimicry
Public
Code for the study: "The perceptual and spatial architecture of Müllerian mimicry in Heliconius butterflies".
MIT License
•0•0•0•0•Updated Mar 5, 2026Mar 5, 2026
catalog
Public template
Catalog app for Imageomics code, data, models, and spaces hosted on GitHub and Hugging Face. Designed for improved discoverability of Imageomics products, the c…
github api open-source
github api open-source data catalog code models inventory open-science spaces
JavaScript
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MIT License
•0•6•7•2•Updated Mar 5, 2026Mar 5, 2026
Image-Datapalooza-2023
Public archive
Repository for the Image Datapalooza 2023 event held at OSU in August 2023.
images workshop-website palooza
images workshop-website palooza
Creative Commons Zero v1.0 Universal
•2•3•8•0•Updated Mar 4, 2026Mar 4, 2026
BeetlePalooza-2024
Public archive
BeetlePalooza collaborative hands-on development event to be held at OSU August 12-15, 2024
workshop-website beetles palooza
workshop-website beetles palooza specimen-images
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•0•3•12•0•Updated Mar 4, 2026Mar 4, 2026
bioclip-image-search-lite
Public
Lightweight BioCLIP image search service using source URLs, FAISS, and DuckDB. Find the most visually similar images across 200M+ samples from the TreeofLife da…
image-search similarity-search faiss
image-search similarity-search faiss duckdb bioclip
Python
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MIT License
•0•0•4•0•Updated Mar 3, 2026Mar 3, 2026
SongSage
Public
A Model Context Protocol (MCP) layer for bioacoustic analysis that augments BirdNET detections with contextual reasoning, uncertainty-aware summaries, and ecolo…
interactive mcp conservation
interactive mcp conservation claude bioacoustics birdnet wildlife-monitoring
Python
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MIT License
•0•0•0•0•Updated Mar 3, 2026Mar 3, 2026
emb-explorer
Public
An interactive tool for classifying images with a pretrained model and exploring clustering results in 2D space.
clustering exploratory-data-analysis eda
clustering exploratory-data-analysis eda data-visualization dimensionality-reduction embedding exploratory-data-visualizations image-exploration
Python
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MIT License
•0•1•0•0•Updated Mar 3, 2026Mar 3, 2026
TaxonoPy
Public
A Python package for efficiently aligning organismal taxonomic hierarchies using the Global Names Verifier
taxonomy alignment hierarchy
taxonomy alignment hierarchy tree-of-life taxonomic-resolution
Python
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MIT License
•0•11•11•3•Updated Feb 27, 2026Feb 27, 2026
fair_drones
Public
The FAIR² Drones Data Standard provides a comprehensive framework for documenting drone-based wildlife datasets, ensuring they are Findable, Accessible, Interop…
uav drone robotics
uav drone robotics standards fair ecology animal-behavior metadata-standards ai-ready dataset-documentation
Creative Commons Zero v1.0 Universal
•0•0•2•0•Updated Feb 25, 2026Feb 25, 2026
mmla
Public
Scripts for MMLA dataset
drones zebra giraffe
drones zebra giraffe
Jupyter Notebook
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MIT License
•1•7•0•11•Updated Feb 20, 2026Feb 20, 2026
TraitBlender
Public
Blender addon for simulating raw datasets under known evolutionary models
images evolution phylogenetic-trees
images evolution phylogenetic-trees phylogenetics simulations raw-data blender-addon 3d-models
Python
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MIT License
•2•3•0•0•Updated Feb 20, 2026Feb 20, 2026
wing-segmentation
Public
Butterfly wing segmentation
rgb segmentation butterfly
rgb segmentation butterfly ruler whitebalance colorchecker wing-segmentation heliconius forewings hindwings
Jupyter Notebook
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MIT License
•2•4•3•3•Updated Feb 19, 2026Feb 19, 2026
Collaborative-distributed-science-guide
Public template
Template guide to collaborative work, including GitHub and Hugging Face workflows. Co-developed with the Imageomics Guide.
git metadata documentation
git metadata documentation data code guide best-practices models projects collaboration
Python
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Creative Commons Zero v1.0 Universal
•0•1•11•0•Updated Feb 18, 2026Feb 18, 2026
BeetleFlow
Public
Official repo for paper "BeetleFlow: An Integrative Deep Learning Pipeline for Beetle Image Processing"
Python
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MIT License
•0•0•2•0•Updated Feb 18, 2026Feb 18, 2026
bioclip-2
Public
Repository for the BioCLIP 2 model project. [NeurIPS'25 Spotlight] BioCLIP 2 is a biological foundation model trained on TreeOfLife-200M. Despite the narrow tra…
computer-vision taxonomy biology
computer-vision taxonomy biology clip knowledge-guided-machine-learning imageomics
Python
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Other
•8•53•2•0•Updated Feb 13, 2026Feb 13, 2026
invasives-project
Public
Repository for the invasive species project as part of the AI & Ecology Course field component in HI.
disease fungi damage
disease fungi damage invasive-species insect leaves invasive
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Feb 12, 2026Feb 12, 2026
BeetleVerse
Public
Jupyter Notebook
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MIT License
•0•0•3•1•Updated Feb 12, 2026Feb 12, 2026
dna-trait-analysis
Public
Goal: to find associations between dna data and visual traits.
Jupyter Notebook
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MIT License
•1•4•7•1•Updated Feb 11, 2026Feb 11, 2026
HDR-SMood-Challenge-sample
Public
Sample Submission Repository for the 2025 HDR Scientific Mood Challenge (Modeling out of distribution).
sample-code out-of-distribution beetles
sample-code out-of-distribution beetles ml-challenge
Jupyter Notebook
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MIT License
•6•1•0•6•Updated Feb 11, 2026Feb 11, 2026
TreeOfLife-toolbox
Public
Source-specific tools for processing data (images) downloaded using distributed downloader and relies on MPI.
face-detection citizen-science image-filtering
face-detection citizen-science image-filtering animal-detection specimen-records tree-of-life imageomics dataset-processing
Jupyter Notebook
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MIT License
•1•3•10•25•Updated Feb 11, 2026Feb 11, 2026
kabr-tools
Public
Modular tools pipeline for annotating animal behavior. These were specifically designed during construction of the KABR dataset, and have been generalized with …
video drone annotation
video drone annotation conservation zebra giraffe cvat animal-behavior-recognition drone-videos
Python
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MIT License
•0•7•16•8•Updated Feb 11, 2026Feb 11, 2026
2026-02-09-osu-online
Public
Software Carpentry Workshop on Version Control with Git and R for Scientific Reproducibility
git r version-control
git r version-control reproducible-research reproducibility workshop-website carpentry-workshop ldw26 lovedataweek
HTML
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Other
•0•0•0•0•Updated Feb 7, 2026Feb 7, 2026
Prompt_CAM
Public
This is an official implementation for PROMPT-CAM: A Simpler Interpretable Transformer for Fine-Grained Analysis (CVPR'25). Explore fine-grained trait distincti…
computer-vision saliency-map fine-grained-classification
computer-vision saliency-map fine-grained-classification interpretable-ai explainable-ai xai interpretable-machine-learning counterfactual-explanations vision-transformer
Jupyter Notebook
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MIT License
•5•70•5•0•Updated Feb 5, 2026Feb 5, 2026
Fish-Vista
Public
Fish-Vista: A Multi-Purpose Dataset for Understanding & Identification of Traits from Images
fish data traits
fish data traits specimen-images trait-identification
Jupyter Notebook
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MIT License
•3•7•0•1•Updated Feb 5, 2026Feb 5, 2026
2018-NEON-beetles-processing
Public
Processing code and exploratory notebooks for BeetlePalooza dataset (2018 NEON Ethanol-preserved Ground Beetles).
annotation images eda
annotation images eda segmentation beetles
Jupyter Notebook
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MIT License
•2•0•0•2•Updated Feb 4, 2026Feb 4, 2026
sum-buddy
Public
Generate and save checksums for all (or certain) contents of given directory.
metadata csv images
metadata csv images checksums deduplication verifier file-verification
Python
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MIT License
•0•3•6•1•Updated Feb 4, 2026Feb 4, 2026
hpc-inference
Public
A high-performance computing solution for efficient batch inference on large-scale image datasets.
Python
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MIT License
•0•0•12•3•Updated Feb 4, 2026Feb 4, 2026
distributed-downloader
Public
MPI-based distributed downloading tool for retrieving data from diverse domains.
url downloader parallel
url downloader parallel dataset-generation mpi-applications
Python
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MIT License
•0•4•3•0•Updated Feb 4, 2026Feb 4, 2026
Andromeda
Public
A website that enables users to explore high-dimensional image data
visualization clustering eda
visualization clustering eda dimensionality-reduction mds data-exploration visual-analytics human-in-the-loop weighted-multi-dimensional-scaling interactive-evaluation
Jupyter Notebook
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MIT License
•1•3•6•1•Updated Feb 4, 2026Feb 4, 2026