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Imageomics: Bringing machine learning to life.

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.

What is the Imageomics Institute?

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

The 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).

Code repositories overview

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. The following gives an overview and useful links.

Imageomics Institute

Institute collaborators


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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  1. INTR INTR Public

    This is an official implementation for [ICLR'24] INTR: Interpretable Transformer for Fine-grained Image Classification.

    Jupyter Notebook 41 4

  2. bioclip bioclip Public

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

    Python 172 14

  3. Andromeda Andromeda Public

    A website that enables users to explore high-dimensional image data

    Jupyter Notebook 2 1

  4. dashboard-prototype dashboard-prototype Public

    Prototype data dashboard for Imageomics Data

    Python 5 2

  5. pybioclip pybioclip Public

    Python package that simplifies using the BioCLIP foundation model.

    Python 22 3

  6. data-workshop-AH-2024 data-workshop-AH-2024 Public

    Repository for Mastering Data Management Workshop at the All Hands 2024.

    Jupyter Notebook 2 2

Repositories

Showing 10 of 63 repositories
  • kabr-tools Public

    Tools for working with data for annotating animal behavior. These were specifically designed during construction of the KABR dataset.

    Imageomics/kabr-tools’s past year of commit activity
    Jupyter Notebook 2 MIT 0 18 9 Updated Dec 11, 2024
  • 2025-02-11-osu-online Public

    Software Carpentry Workshop on Version Control with Git and R for Scientific Reproducibility

    Imageomics/2025-02-11-osu-online’s past year of commit activity
    HTML 0 0 0 0 Updated Dec 11, 2024
  • snakemake-workshop Public

    Lesson on creating a Snakemake Workflow with an Imageomics emphasis

    Imageomics/snakemake-workshop’s past year of commit activity
    1 0 4 0 Updated Dec 10, 2024
  • pybioclip Public

    Python package that simplifies using the BioCLIP foundation model.

    Imageomics/pybioclip’s past year of commit activity
    Python 22 MIT 3 4 1 Updated Dec 9, 2024
  • Imageomics-guide Public

    Imageomics-focused guide to collaborative work, including GitHub and Hugging Face workflows.

    Imageomics/Imageomics-guide’s past year of commit activity
    Python 1 CC0-1.0 0 1 0 Updated Dec 3, 2024
  • wing-segmentation Public

    Butterfly wing segmentation

    Imageomics/wing-segmentation’s past year of commit activity
    Jupyter Notebook 0 MIT 0 1 4 Updated Dec 2, 2024
  • animal-id Public

    Currently add viewpoint classifier only, but will update entire pipeline

    Imageomics/animal-id’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Dec 2, 2024
  • data-workshop-AH-2024 Public

    Repository for Mastering Data Management Workshop at the All Hands 2024.

    Imageomics/data-workshop-AH-2024’s past year of commit activity
    Jupyter Notebook 2 CC0-1.0 2 0 0 Updated Nov 26, 2024
  • HDR-anomaly-challenge Public

    Repository for Imageomics' CodaBench challenge as part of the HDR Anomaly ML Challenge.

    Imageomics/HDR-anomaly-challenge’s past year of commit activity
    Python 4 MIT 1 1 1 Updated Nov 26, 2024
  • HDR-anomaly-challenge-sample Public

    Sample Submission Repository for the 2024 HDR Anomaly Challenge

    Imageomics/HDR-anomaly-challenge-sample’s past year of commit activity
    Jupyter Notebook 3 MIT 1 0 0 Updated Nov 25, 2024

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