Imageomics Institute

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105 repositories

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•10•11•3•Updated Feb 16, 2026Feb 16, 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 clip knowledge-guided-machine-learning imageomics
Python
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Other
•8•51•2•0•Updated Feb 13, 2026Feb 13, 2026
emb-explorer
Public
An interactive tool for classifying images with a pretrained model and exploring clustering results in 2D space.
Python
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MIT License
•0•0•2•5•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 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•8•2•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 ml-challenge
Jupyter Notebook
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MIT License
•5•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 animal-detection specimen-records tree-of-life imageomics dataset-processing
Jupyter Notebook
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MIT License
•1•3•11•26•Updated Feb 11, 2026Feb 11, 2026
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•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 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
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•9•0•Updated Feb 6, 2026Feb 6, 2026
Prompt_CAM
Public
This is an official implementation for PROMPT-CAM: A Simpler Interpretable Transformer for Fine-Grained Analysis (CVPR'25)
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•68•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 specimen-images trait-identification
Jupyter Notebook
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MIT License
•3•6•0•2•Updated Feb 5, 2026Feb 5, 2026
mmla
Public
Scripts for MMLA dataset
drones zebra giraffe
Jupyter Notebook
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MIT License
•1•7•1•12•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 segmentation beetles
Jupyter Notebook
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MIT License
•2•0•1•3•Updated Feb 4, 2026Feb 4, 2026
sum-buddy
Public
Generate and save checksums for all (or certain) contents of given directory.
metadata csv images checksums deduplication verifier file-verification
Python
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MIT License
•0•3•7•2•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•13•4•Updated Feb 4, 2026Feb 4, 2026
distributed-downloader
Public
MPI-based distributed downloading tool for retrieving data from diverse domains.
url downloader parallel dataset-generation mpi-applications
Python
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MIT License
•0•4•4•1•Updated Feb 4, 2026Feb 4, 2026
Andromeda
Public
A website that enables users to explore high-dimensional image data
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•7•2•Updated Feb 4, 2026Feb 4, 2026
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•1•1•Updated Feb 4, 2026Feb 4, 2026
bioclip-vector-db
Public
Vector database training data retrieval of BioCLIP-embedded nearest neighbors.
Python
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MIT License
•1•0•13•6•Updated Feb 4, 2026Feb 4, 2026
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 sav…
github inventory google-sheets api-integration repo-records organization-based-tools
Python
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MIT License
•0•2•6•1•Updated Feb 4, 2026Feb 4, 2026
biocap
Public
Repository for the BioCAP model project. [ICLR'26] Biological foundation model trained on the TreeOfLife-10M dataset paired with a new TreeOfLife-10M Captions d…
computer-vision taxonomy biology clip knowledge-guided-machine-learning imageomics synthetic-captions
Python
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Other
•0•5•1•1•Updated Feb 4, 2026Feb 4, 2026
FAIR4AI-checklists
Public
FAIR4AI Working Group repo for organization, planning, and development.
Python
•0•2•7•1•Updated Feb 3, 2026Feb 3, 2026
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 Jan 29, 2026Jan 29, 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 data catalog code models inventory open-science spaces
JavaScript
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MIT License
•0•5•5•0•Updated Jan 28, 2026Jan 28, 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•8•0•Updated Jan 26, 2026Jan 26, 2026
global-egg-trait
Public
This repository contains a computer vision pipeline for detecting, segmenting, and cropping eggs from biological images using Grounding DINO & SAM2.
detection segmentation eggs traits palooza
Python
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MIT License
•1•0•5•1•Updated Jan 21, 2026Jan 21, 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 standards fair ecology animal-behavior metadata-standards ai-ready dataset-documentation
Creative Commons Zero v1.0 Universal
•0•0•2•0•Updated Jan 16, 2026Jan 16, 2026
.github
Public
MIT License
•1•0•0•0•Updated Jan 16, 2026Jan 16, 2026