Imageomics Institute

All

101 repositories

mmla
Public
Scripts for MMLA dataset
drones zebra giraffe
Jupyter Notebook
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MIT License
•0•5•0•11•Updated Jan 6, 2026Jan 6, 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 ml-challenge
Jupyter Notebook
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MIT License
•1•1•0•4•Updated Jan 6, 2026Jan 6, 2026
SST
Public
Official repo for paper "Static Segmentation by Tracking: A Frustratingly Label-Efficient Approach to Fine-Grained Segmentation"
computer-vision biology trait-segmentation specimen-images
Jupyter Notebook
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MIT License
•3•10•0•6•Updated Jan 5, 2026Jan 5, 2026
bioclip-2
Public
Repository for the BioCLIP 2 model project. [NeurIPS'25 Spotlight]
computer-vision taxonomy biology clip knowledge-guided-machine-learning imageomics
Python
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Other
•8•43•2•1•Updated Jan 3, 2026Jan 3, 2026
cautious-robot
Public
Simple images from CSV downloader that runs and records checksums on downloaded image folder.
csv download images checksums verifier downsized
Python
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MIT License
•1•5•9•2•Updated Dec 31, 2025Dec 31, 2025
repo-exporter
Public
A Python script that collects key info (Name, description, creation date, last updated date, contributors, etc.) from all repos in a GitHub organization and saves it to a color-coded Google Sheet file of choice.
github inventory google-sheets api-integration repo-records organization-based-tools
Python
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MIT License
•0•2•5•0•Updated Dec 19, 2025Dec 19, 2025
Imageomics-guide
Public
Imageomics-focused guide to collaborative work, including GitHub and Hugging Face workflows.
git metadata documentation data code guide best-practices models projects collaboration
Python
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Creative Commons Zero v1.0 Universal
•0•4•7•1•Updated Dec 19, 2025Dec 19, 2025
kabr-tools
Public
Tools for working with data for annotating animal behavior. These were specifically designed during construction of the KABR dataset.
video drone annotation conservation zebra giraffe cvat animal-behavior-recognition drone-videos
Python
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MIT License
•0•7•15•7•Updated Dec 19, 2025Dec 19, 2025
2026-02-09-osu-online
Public
Software Carpentry Workshop on Version Control with Git and R for Scientific Reproducibility
git r version-control reproducible-research reproducibility workshop-website carpentry-workshop ldw26 lovedataweek
HTML
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Other
•0•0•0•0•Updated Dec 19, 2025Dec 19, 2025
invasives-project
Public
Repository for the invasive species project as part of the AI & Ecology Course field component in HI.
disease fungi damage invasive-species insect leaves invasive
Jupyter Notebook
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MIT License
•0•0•0•1•Updated Dec 18, 2025Dec 18, 2025
catalog
Public
Catalog app for Imageomics code, data, models, and spaces hosted on GitHub and Hugging Face.
github api open-source data catalog code models inventory open-science spaces
JavaScript
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MIT License
•0•2•6•0•Updated Dec 18, 2025Dec 18, 2025
carabidae_beetle_processing
Public
Pipeline for processing, analyzing, and validating beetle specimen images and morphometric measurements from NEON (National Ecological Observatory Network) beetle specimens (specifically for 2018 NEON Beetles and Hawaii Beetles datasets).
images annotations segmentation measurements morphometrics ecology elytra traits neon-data beetles
Jupyter Notebook
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MIT License
•1•0•0•0•Updated Dec 18, 2025Dec 18, 2025
ecoCroissant
Public
Repository for developing croissant-based biodiversity metadata schema following FAIR4AI principles.
0•1•0•1•Updated Dec 18, 2025Dec 18, 2025
bioclip-vector-db
Public
Vector database training data retrieval of BioCLIP-embedded nearest neighbors.
Python
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MIT License
•1•0•13•4•Updated Dec 18, 2025Dec 18, 2025
TaxonoPy
Public
A Python package for efficiently aligning organismal taxonomic hierarchies using the Global Names Verifier
taxonomy alignment hierarchy tree-of-life taxonomic-resolution
Python
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MIT License
•0•7•8•2•Updated Dec 17, 2025Dec 17, 2025
TreeOfLife-toolbox
Public
Source-specific tools for processing data (images) downloaded using distributed downloader and relies on MPI.
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•9•24•Updated Dec 16, 2025Dec 16, 2025
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 data code guide best-practices models projects collaboration
Python
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Creative Commons Zero v1.0 Universal
•0•1•10•1•Updated Dec 16, 2025Dec 16, 2025
naturelab
Public
Bridging Digital and Natural Worlds at The Wilds
drone biology gps-tracker ecology multi-modal camera-traps bioacoustics
Jupyter Notebook
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MIT License
•2•2•0•0•Updated Dec 16, 2025Dec 16, 2025
biocap
Public
Repository for the BioCAP model project.
computer-vision taxonomy biology clip knowledge-guided-machine-learning imageomics synthetic-captions
Python
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Other
•0•1•0•0•Updated Dec 16, 2025Dec 16, 2025
phylonn
Public
Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks
Python
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MIT License
•1.2k•0•0•1•Updated Dec 15, 2025Dec 15, 2025
vector-db-on-demand
Public
On demand vector db indexing capabilities with fast neighbor retrieval
MIT License
•0•0•0•0•Updated Dec 14, 2025Dec 14, 2025
HDR-SMood-Challenge
Public
Repository for Imageomics' CodaBench challenge as part of the HDR Scientific Mood ML Challenge.
out-of-distribution beetles ml-challenge
Python
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MIT License
•0•5•0•0•Updated Dec 11, 2025Dec 11, 2025
bioclip-app
Public
0•1•0•0•Updated Dec 6, 2025Dec 6, 2025
phylo-diffusion
Public
Implementation of "Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution" [ECCV 2024]
fish biology evolution birds species phylogeny tree-of-life diffusion-models knowledge-guided hierarchical-conditioning
Python
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MIT License
•1•6•1•0•Updated Dec 6, 2025Dec 6, 2025
pygbif
Public
GBIF Python client
Python
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MIT License
•36•0•0•1•Updated Dec 5, 2025Dec 5, 2025
.github
Public
MIT License
•1•0•0•0•Updated Dec 5, 2025Dec 5, 2025
mimicry-madness
Public
Project repo for mimicry exploration during FuncaPalooza 2025!
images traits snakes mimicry mimics moths wasps palooza embedding-exploration
Jupyter Notebook
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MIT License
•0•1•0•1•Updated Dec 5, 2025Dec 5, 2025
h5-image-explorer
Public
Preview image sets from a lookup table extracted from a dataset made up of sharded HDF5 files.
images hdf5 image-preview hdf5-visualization
JavaScript
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MIT License
•0•1•0•0•Updated Dec 5, 2025Dec 5, 2025
pybioclip
Public
Python package that simplifies using the BioCLIP foundation model.
taxonomy biology cv image-classification clip command-line-interface bioclip knowledge-guided
Python
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MIT License
•10•57•9•1•Updated Dec 5, 2025Dec 5, 2025
Imageomics-NeurIPS-2025
Public
Imageomics: Discovering Biological Knowledge from Images Using AI workshop at NeurIPS 2025
workshop-website
HTML
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Creative Commons Zero v1.0 Universal
•0•1•0•0•Updated Nov 27, 2025Nov 27, 2025