Imageomics Institute

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96 repositories

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
•3•58•3•0•Updated Nov 26, 2025Nov 26, 2025
catalog
Public
Repository for Imageomics data, model, and code catalog.
api data catalog models inventory spaces keyword-search discoverability imageomics searchability
JavaScript
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MIT License
•0•2•7•1•Updated Nov 26, 2025Nov 26, 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•1•9•21•Updated Nov 26, 2025Nov 26, 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•1•Updated Nov 25, 2025Nov 25, 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•1•1•0•Updated Nov 25, 2025Nov 25, 2025
dna-trait-analysis
Public
Goal: to find associations between dna data and visual traits.
Jupyter Notebook
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MIT License
•0•4•7•0•Updated Nov 25, 2025Nov 25, 2025
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•1•Updated Nov 25, 2025Nov 25, 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 25, 2025Nov 25, 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•8•1•Updated Nov 25, 2025Nov 25, 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•16•7•Updated Nov 24, 2025Nov 24, 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•5•9•2•Updated Nov 24, 2025Nov 24, 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•6•1•Updated Nov 24, 2025Nov 24, 2025
char-sim
Public
Pipeline to create model for comparing character state descriptions including ontology similarity
Jupyter Notebook
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MIT License
•1•0•6•0•Updated Nov 24, 2025Nov 24, 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•56•9•2•Updated Nov 22, 2025Nov 22, 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 Nov 21, 2025Nov 21, 2025
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•11•3•Updated Nov 21, 2025Nov 21, 2025
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•42•1•1•Updated Nov 19, 2025Nov 19, 2025
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•4•Updated Nov 17, 2025Nov 17, 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•2•Updated Nov 14, 2025Nov 14, 2025
mmla
Public
Scripts for MMLA dataset
drones zebra giraffe
Jupyter Notebook
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MIT License
•0•4•0•9•Updated Nov 14, 2025Nov 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•3•0•0•Updated Nov 12, 2025Nov 12, 2025
bioclip-vector-db
Public
Vector database training data retrieval of BioCLIP-embedded nearest neighbors.
Python
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MIT License
•1•0•7•3•Updated Nov 12, 2025Nov 12, 2025
Finer-CAM
Public
This is an official implementation for Finer-CAM: Spotting the Difference Reveals Finer Details for Visual Explanation. [CVPR'25]
computer-vision visualizations class-activation-maps fine-grained-classification explainable-ai xai saliency-maps vision-transformers
Jupyter Notebook
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Apache License 2.0
•4•45•0•0•Updated Nov 10, 2025Nov 10, 2025
Butterfly-mimicry
Public
Exploring the influence of acuity on classification accuracy and mimicry in Heliconius butterflies.
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Nov 6, 2025Nov 6, 2025
phylonn
Public
Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks
Python
•1.2k•0•0•1•Updated Nov 5, 2025Nov 5, 2025
data-workshop-AH-2024
Public
Repository for Mastering Data Management Workshop at the All Hands 2024.
documentation data-validation eda provenance data-analysis data-management checksums
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•2•2•1•0•Updated Oct 25, 2025Oct 25, 2025
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•2•0•Updated Oct 22, 2025Oct 22, 2025
KABR
Public
Centralized resource to describe and link out to all components of the KABR project (Kenyan Animal Behavior Recognition).
behavior data tools code models pipelines kabr ungulates mini-scenes
HTML
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Oct 17, 2025Oct 17, 2025
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
Python
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MIT License
•1•0•0•2•Updated Oct 6, 2025Oct 6, 2025
HDR-anomaly-challenge-sample
Public
Sample Submission Repository for the 2024 HDR Anomaly Challenge
sample-code anomaly-detection butterflies ml-challenge
Jupyter Notebook
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MIT License
•4•6•1•5•Updated Sep 23, 2025Sep 23, 2025