Imageomics repositories

141 repositories

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
•
MIT License
•0•6•10•2•Updated Sep 22, 2026Sep 22, 2026
repo-exporter
Public
Python scripts that collect key info (Name, description, creation date, last updated date, contributors, etc.) from all repos in a GitHub or Hugging Face organi…
github api metadata
github api metadata inventory google-sheets repository-management api-integration fair-principles huggingface metadata-export
Python
•
MIT License
•0•2•7•5•Updated Sep 22, 2026Sep 22, 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
•
MIT License
•0•10•6•4•Updated Sep 21, 2026Sep 21, 2026
SST
Public
Official repo for paper "Static Segmentation by Tracking: A Frustratingly Label-Efficient Approach to Fine-Grained Segmentation". Ideal for specimen image trait…
computer-vision biology trait-segmentation
computer-vision biology trait-segmentation specimen-images
Jupyter Notebook
•
MIT License
•3•14•5•6•Updated Sep 20, 2026Sep 20, 2026
OpenCite
Public
Web-based tool for generating consistent CITATION.cff and .zenodo.json files from a single structured input form, reducing metadata inconsistencies across resea…
metadata attribution citation
metadata attribution citation provenance fair zenodo cff-format cff-citation-validation
JavaScript
•
MIT License
•0•0•8•1•Updated Sep 19, 2026Sep 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
•
Creative Commons Zero v1.0 Universal
•1•1•14•1•Updated Sep 19, 2026Sep 19, 2026
features-as-field-guides
Public
A fork of Sparse autoencoders for vision (saev) for dichotomous key discovery
Python
•
MIT License
•12•0•0•5•Updated Sep 19, 2026Sep 19, 2026
bioclip
Public
This is the repository for the BioCLIP model and the TreeOfLife-10M dataset [CVPR'24 Oral, Best Student Paper].
computer-vision taxonomy clip
computer-vision taxonomy clip knowledge-guided-machine-learning imageomics
Python
•
Other
•26•278•4•1•Updated Sep 18, 2026Sep 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
•
Other
•12•98•3•0•Updated Sep 17, 2026Sep 17, 2026
hdr-species-map-explorer
Public
Classroom species distribution explorer (GBIF + biogeography + climate overlays)
education web-app data-exploration
education web-app data-exploration biodiversity hdr environmental-science species-distribution imageomics
HTML
•
MIT License
•0•0•0•0•Updated Sep 15, 2026Sep 15, 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
•
MIT License
•7•78•3•2•Updated Sep 14, 2026Sep 14, 2026
hpc-inference
Public
A high-performance computing solution for efficient batch inference on large-scale image datasets.
Python
•
MIT License
•0•0•12•2•Updated Sep 11, 2026Sep 11, 2026
saev
Public
Sparse autoencoders for vision
computer-vision sparse-autoencoders interpretability
computer-vision sparse-autoencoders interpretability
Python
•
MIT License
•12•67•7•20•Updated Sep 4, 2026Sep 4, 2026
HypeRGB
Public
Multimodal model(s) integrating hyperspectral and RGB image data to classify species ID from herbarium specimens
1•0•0•0•Updated Sep 3, 2026Sep 3, 2026
BeetleFlow
Public
Official repo for paper "BeetleFlow: An Integrative Deep Learning Pipeline for Beetle Image Processing"
computer-vision deep-learning image-processing
computer-vision deep-learning image-processing object-detection image-segmentation entomology imageomics
Python
•
MIT License
•1•0•0•8•Updated Sep 1, 2026Sep 1, 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
•
MIT License
•1•7•11•27•Updated Aug 31, 2026Aug 31, 2026
imageomics.github.io
Public
Repository to host the Imageomics Institute's website.
HTML
•
Creative Commons Attribution 4.0 International
•0•0•1•1•Updated Aug 31, 2026Aug 31, 2026
Imageomics-guide
Public
Imageomics-focused guide to collaborative work, including GitHub and Hugging Face workflows.
git metadata documentation
git metadata documentation data code guide best-practices models projects collaboration
Python
•
Creative Commons Zero v1.0 Universal
•0•6•6•1•Updated Aug 28, 2026Aug 28, 2026
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
•
MIT License
•0•1•8•0•Updated Aug 26, 2026Aug 26, 2026
beetle-imaging-procedure
Public
Standard Operating Procedure (SOP) for Imaging Pinned Ground Beetles at the NEON Biorepository.
MIT License
•0•1•0•0•Updated Aug 26, 2026Aug 26, 2026
simple-localized-counterfactuals
Public
Source code for the CVPR HOW workshop paper
Jupyter Notebook
•
MIT License
•0•0•0•19•Updated Aug 21, 2026Aug 21, 2026
PlotDiversiVision
Public
Florapalooza plot diversity image segmentation and bioclip identification
Python
•
Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Aug 21, 2026Aug 21, 2026
got-milk-monarchs
Public
FloraPalooza project for detecting Monarch caterpillar chewing damage on Milkweed plants.
logistic-regression caterpillar leaves
logistic-regression caterpillar leaves monarch milkweed palooza leaf-damage
Python
•
MIT License
•0•0•0•0•Updated Aug 20, 2026Aug 20, 2026
SAtrEes
Public
FloraPalooza project to extract land-use history from RGB images of tree crowns.
rgb land-use disturbance
rgb land-use disturbance palooza tree-crowns harvard-forest flyover-data
R
•
MIT License
•0•0•1•0•Updated Aug 20, 2026Aug 20, 2026
AgDamage
Public
FloraPalooza project for detecting herbicide damage to weeds and crops.
MIT License
•0•0•0•0•Updated Aug 20, 2026Aug 20, 2026
cautious-robot
Public
Simple images from CSV downloader that runs and records checksums on downloaded image folder.
cli csv download
cli csv download images fair reproducibility checksums data-access verifier downsized
Python
•
MIT License
•1•5•18•5•Updated Aug 19, 2026Aug 19, 2026
lca
Public
An independent implementation of the Local Clusters and their Alternatives (LCA) graph-based ID curation algoritihm
Jupyter Notebook
•
Apache License 2.0
•6•1•0•0•Updated Aug 15, 2026Aug 15, 2026
pybioclip
Public
Python package and CLI that simplifies using the BioCLIP family of foundation models.
taxonomy biology cv
taxonomy biology cv image-classification clip command-line-interface bioclip knowledge-guided
Python
•
MIT License
•14•67•14•3•Updated Aug 15, 2026Aug 15, 2026
BeetleVerse
Public
Benchmark suite for evaluating vision models on ground beetle classification, with evaluation notebooks and results for genus- and species-level classification,…
benchmarking neon evaluation
benchmarking neon evaluation image-classification multimodal beetles carabidae palooza
Jupyter Notebook
•
MIT License
•0•0•3•2•Updated Aug 14, 2026Aug 14, 2026
CarabidImaging
Public
Image Processing for NEON Biorepository ground beetle imaging.
computer-vision neon metadata-validation
computer-vision neon metadata-validation natural-history-collections carabidae specimen-digitization batch-imaging
R
•
MIT License
•0•2•1•3•Updated Aug 14, 2026Aug 14, 2026

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Imageomics Institute

All

141 repositories

emb-explorer

repo-exporter

catalog

SST

OpenCite

Collaborative-distributed-science-guide

features-as-field-guides

bioclip

bioclip-2

hdr-species-map-explorer

Prompt_CAM

hpc-inference

saev

HypeRGB

BeetleFlow

TreeOfLife-toolbox

imageomics.github.io

Imageomics-guide

bioclip-ecosystem

beetle-imaging-procedure

simple-localized-counterfactuals

PlotDiversiVision

got-milk-monarchs

SAtrEes

AgDamage

cautious-robot

lca

pybioclip

BeetleVerse

CarabidImaging

Repositories list

141 repositories