Imageomics Institute
- 139 followers
- United States of America
- https://imageomics.org
- @imageomics
- company/imageomics-institute
- imageomics
- https://hf.co/imageomics
The Imageomics Institute GitHub organization hosts the development and distribution of a collection of open-source ML tools used to study the biological information encoded in images and videos integrated with structured biological knowledge. All Imageomics code, data, models, and demos hosted on GitHub or Hugging Face are searchable through the Imageomics Catalog:
The Imageomics Institute is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under Award #2118240 (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). It started in Oct 2021.
You can find a full mission, vision, and abstract under the Imageomics website's About page. In short, the vision of the Institute is to "establish a new scientific field called imageomics that harnesses revolutions in data science and computing, as well as the rapidly expanding collections of biological image data, in order to accelerate biological understanding of phenotypic traits extracted from images of organisms."
History leading to the InstituteThe inception and research of the Imageomics Institute builds heavily on the "Biology-Guided Neural Networks for Discovering Phenotypic Traits" (BGNN) project, also funded by the US National Science Foundation. BGNN itself built in part on the Phenoscape project (funded by NSF multiple times), which started in 2007 and was incubated at the NSF-funded National Evolutionary Synthesis Center (NESCent).
Due to the history (see above) and highly collaborative and cross-disciplinary nature of the Institute, important software products and other code repositories are distributed over several organizations in GitHub, in addition to the ones found here. These early imageomics projects are listed and linked below under their organizations.
Disclaimer: Any opinions, findings and conclusions or recommendations expressed in the materials here are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
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Repositories
- Collaborative-distributed-science-guide Public template
Template guide to collaborative work, including GitHub and Hugging Face workflows. Co-developed with the Imageomics Guide.
- features-as-field-guides Public Forked from Imageomics/saev
A fork of Sparse autoencoders for vision (saev) for dichotomous key discovery
- 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 training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction.
- hdr-species-map-explorer Public
Classroom species distribution explorer (GBIF + biogeography + climate overlays)
- 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 distinctions between different specified species.
- 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 organization and save it to a color-coded Google Sheet file of choice.
- hpc-inference Public
A high-performance computing solution for efficient batch inference on large-scale image datasets.
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