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Imageomics

58 indexed repositories · View on GitHub

bioclip
This is the repository for the BioCLIP model and the TreeOfLife-10M dataset [CVPR'24 Oral, Best Student Paper].

Python · 278 stars
bioclip-2
Repository for the BioCLIP 2 model project. [NeurIPS'25 Spotlight] BioCLIP 2 is a biological foundation model trained on TreeOfLife-200M....

Python · 93 stars
Prompt_CAM
This is an official implementation for PROMPT-CAM: A Simpler Interpretable Transformer for Fine-Grained Analysis (CVPR'25). Explore fine-...

Jupyter Notebook · 78 stars
pybioclip
Python package and CLI that simplifies using the BioCLIP family of foundation models.

Python · 67 stars
saev
Sparse autoencoders for vision

Python · 66 stars
Finer-CAM
This is an official implementation for Finer-CAM: Spotting the Difference Reveals Finer Details for Visual Explanation. [CVPR'25] Better ...

Jupyter Notebook · 53 stars
TaxonoPy
A Python package for efficiently aligning organismal taxonomic hierarchies using the Global Names Verifier

Python · 19 stars
SST
Official repo for paper "Static Segmentation by Tracking: A Frustratingly Label-Efficient Approach to Fine-Grained Segmentation". Ideal f...

Jupyter Notebook · 14 stars
biobench
Computer vision benchmark for evolutionary biology-related tasks.

Python · 10 stars
kabr-tools
Modular tools pipeline for annotating animal behavior. These were specifically designed during construction of the KABR dataset, and have...

Python · 10 stars
catalog
Catalog app for Imageomics code, data, models, and spaces hosted on GitHub and Hugging Face. Designed for improved discoverability of Ima...

JavaScript · 10 stars
phylo-diffusion
Implementation of "Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution" [ECCV 2024]

Python · 8 stars
mmla
Scripts for MMLA dataset

Jupyter Notebook · 7 stars
wildwing
Autonomous UAS Software for In Situ Imageomics Missions

HTML · 7 stars
TreeOfLife-toolbox
Source-specific tools for processing data (images) downloaded using distributed downloader and relies on MPI.

Jupyter Notebook · 7 stars
dashboard-prototype
Prototype data dashboard for Imageomics Data

Python · 6 stars
wing-segmentation
Butterfly wing segmentation

Jupyter Notebook · 6 stars
Imageomics-guide
Imageomics-focused guide to collaborative work, including GitHub and Hugging Face workflows.

Python · 6 stars
emb-explorer
An interactive tool for classifying images with a pretrained model and exploring clustering results in 2D space.

Python · 6 stars
FuncaPalooza-2025
FuncaPalooza: collaborative hands-on event for extracting functional traits from images at OSU, Aug 18-21, 2025.

5 stars
38 more repositories live on View on GitHub

Beginner friendly Everything

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Move download verification functions into `buddy_check.py` Open

structure

Imageomics/cautious-robot#62 · 1 assignee · Opened Jun 8, 2026
Create `roll_call` module Open

question structure

Imageomics/cautious-robot#61 · 1 assignee · Opened Jun 8, 2026
Add provenance files Open

documentation

Imageomics/CarabidImaging#3 · 1 assignee · Opened Jun 4, 2026
Place linting in a separate workflow Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 58/100

Imageomics/cautious-robot#57 · 1 comment · Opened Jun 4, 2026
Update paper links to publications in proceedings Open

Difficulty 1/5 Under an hour Newbie friendliness 65/100

Imageomics/bioclip-ecosystem#50 · Opened Jun 4, 2026
HF Demo Space for Precalculated Embedding App Open

design enhancement

Imageomics/emb-explorer#31 · 6 comments · 1 assignee · Opened Jun 1, 2026
Sort outputs Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

Imageomics/sum-buddy#43 · 1 reaction · Opened May 29, 2026
Centralize default policy configs Open

structure

Difficulty 3/5 1-2 days Newbie friendliness 55/100

Imageomics/sum-buddy#42 · Opened May 29, 2026
Add new BioCLIP-HC models to model page Open

update

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

Imageomics/bioclip-ecosystem#43 · Opened May 27, 2026
Add TOL Embeddings and FAISS index datasets to data page Open

update

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

Imageomics/bioclip-ecosystem#42 · Opened May 27, 2026
Add "Interpret Model Predictions/Inference/Results" button Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

Imageomics/bioclip-ecosystem#40 · Opened May 26, 2026
Review request: v0.2.0 release Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

Imageomics/camera-trap-geolocation#1 · 1 comment · Opened May 22, 2026
Common names cache dir dead code to remove Open

Difficulty 1/5 Under an hour Newbie friendliness 78/100

Imageomics/TaxonoPy#35 · Opened May 21, 2026
IO inaccuracies in documentation Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 55/100

Imageomics/TaxonoPy#34 · Opened May 21, 2026
Stand up an API-only sibling Space for programmatic clients Open

epic

Imageomics/bioclip-image-search-lite#38 · 1 assignee · Opened May 21, 2026
Add a "Community" tab Open

design enhancement

Imageomics/bioclip-ecosystem#38 · 1 comment · 1 assignee · Opened May 18, 2026
Reproducibility and source dataset alignment Open

Imageomics/BeetleVerse#7 · 1 assignee · Opened May 13, 2026
Develop documentation Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 45/100

Imageomics/SST#24 · 2 reactions · Opened May 13, 2026
Expand ability to support adaptors for other repository platforms Open

Difficulty 5/5 Over a week Newbie friendliness 28/100

Imageomics/catalog#93 · 9 comments · Opened May 7, 2026
Update GH PR Guide Page Open

documentation enhancement

Difficulty 3/5 1-2 days Newbie friendliness 65/100

Imageomics/Collaborative-distributed-science-guide#73 · Opened May 5, 2026
Add reference to CV4animals paper Open

documentation

Imageomics/milu-deer-bioacoustics#7 · 1 assignee · Opened May 4, 2026
Option to address "clutter" Open

question

Difficulty 5/5 Over a week Newbie friendliness 35/100

Imageomics/catalog#90 · 2 comments · Opened May 1, 2026
Add index-build pipeline for the lite service Open

data documentation

Imageomics/bioclip-image-search-lite#36 · 1 assignee · Opened May 1, 2026
Introduce cautious concurrency Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

Imageomics/cautious-robot#55 · 1 reaction · Opened May 1, 2026
Deploy workflow blocked by `prod` ruleset; switch to deploy key bypass Open

bug deploy

Imageomics/bioclip-image-search-lite#31 · 1 assignee · Opened Apr 30, 2026
Consider adding more context for citation formatting Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

Imageomics/Collaborative-distributed-science-guide#71 · Opened Apr 29, 2026
Make a docs site Open

documentation enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

Imageomics/sum-buddy#37 · 1 reaction · Opened Apr 28, 2026
Consider reframing HF Dataset Upload Guide as a more general HF Upload Guide Open

Difficulty 2/5 1-3 hours Newbie friendliness 58/100

Imageomics/Collaborative-distributed-science-guide#68 · 1 comment · Opened Apr 27, 2026
markdownlint update resulting in errors listed for Command Line Cheat Sheet page Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

Imageomics/Collaborative-distributed-science-guide#67 · Opened Apr 27, 2026
Add TAR support and decide how nested archives are dealt with. Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

Imageomics/sum-buddy#34 · Opened Apr 27, 2026
Use local metadata file generation to check HF repo Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

Imageomics/sum-buddy#33 · 11 comments · Opened Apr 26, 2026
Package for PyPI publication Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

Imageomics/SST#22 · 1 reaction · Opened Apr 24, 2026
Consider addition to predict from list of classes feature Open

Difficulty 5/5 Over a week Newbie friendliness 45/100

Imageomics/pybioclip#195 · 3 comments · 1 reaction · Opened Apr 23, 2026
Re-train FAISS index to include FathomNet and BIOSCAN embeddings Open

data

Imageomics/bioclip-image-search-lite#27 · 1 reaction · 1 assignee · Opened Apr 22, 2026
CLI predict reloads model on every invocation, consider persistent session Open

Difficulty 5/5 Over a week Newbie friendliness 45/100

Imageomics/pybioclip#193 · 4 comments · Opened Apr 22, 2026
Set up docs site Open

documentation

Imageomics/emb-explorer#28 · 1 reaction · 1 assignee · Opened Apr 22, 2026
PyPI release for emb-explorer Open

documentation enhancement

Imageomics/emb-explorer#27 · 2 comments · 1 assignee · Opened Apr 22, 2026
Windows uv venv activation Open

documentation enhancement

Imageomics/emb-explorer#26 · 1 comment · 1 reaction · 1 assignee · Opened Apr 22, 2026
Add parquet format as an output for embeddings? Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

Imageomics/pybioclip#177 · 1 comment · Opened Apr 16, 2026
Review test suite for trivial tests Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

Imageomics/open-set-atlas#1 · 3 comments · Opened Mar 30, 2026
Windows compatibility issues with installation and embedding pipeline Open

bug dependencies documentation enhancement

Imageomics/emb-explorer#21 · 1 assignee · Opened Mar 25, 2026
Optimize test suite with shared classifiers and GPU support Open

Difficulty 4/5 3-5 days Newbie friendliness 68/100

Imageomics/pybioclip#168 · 3 comments · Opened Mar 19, 2026
Support prediction from pre-computed image embeddings Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

Imageomics/pybioclip#167 · 4 comments · Opened Mar 19, 2026
Docs dependencies Open

dependencies documentation

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Imageomics/kabr-tools#119 · Opened Mar 4, 2026
Tooling consideration for docs site Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

Imageomics/Collaborative-distributed-science-guide#58 · 1 comment · Opened Mar 2, 2026
Add other related software projects Open

update

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

Imageomics/bioclip-ecosystem#23 · 2 comments · Opened Feb 20, 2026
Trace command package version silent cache misses Open

enhancement

Imageomics/TaxonoPy#29 · 1 assignee · Opened Feb 19, 2026
Investigate SAM 3 for combined detection and segmentation; integrate if viable Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Imageomics/wing-segmentation#10 · Opened Feb 19, 2026
Add loading state message for cold starts / Space wake-ups Open

frontend

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Imageomics/bioclip-image-search-lite#16 · Opened Feb 19, 2026
Cache BioCLIP-2 model weights in HF data repo to speed up Space cold starts Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

Imageomics/bioclip-image-search-lite#12 · Opened Feb 18, 2026

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