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@Arcadia-Science

Arcadia Science

README.md

Welcome to @Arcadia-Science!

At Arcadia, one of our central tenets is that our science should be maximally useful. Computational tasks are embedded in all aspects of our scientific inquiry, so we need our computing strategies to be maximally useful too. What does this mean? In addition to aligning with scientific priorities across Arcadia, we believe that useful computing is ✨ innovative, 👩‍💻usable, 🔁 reproducible.

Popular repositories Loading

  1. agentic-pymol agentic-pymol Public

    A Model Context Protocol (MCP) server that exposes PyMOL as a typed tool surface to your agent (Claude Code/Desktop, Codex, or any MCP-compatible client)

    Python 108 21

  2. glass-box-umap glass-box-umap Public

    Python package for making UMAP interpretable with exact feature contributions

    Python 55 3

  3. ProteinCartography ProteinCartography Public

    A pipeline to build similarity maps of protein space

    Jupyter Notebook 49 15

  4. readlif readlif Public archive

    Leica Image Format (LIF) file reader for Python

    Python 40 14

  5. metagenomics metagenomics Public

    A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies

    Nextflow 39 5

  6. seqqc seqqc Public

    A Nextflow pipeline to identify quality control issues with new sequencing data.

    Groovy 30

Repositories

Showing 10 of 146 repositories
  • accounting-for-nonlinear-phenotypes Public
    Arcadia-Science/accounting-for-nonlinear-phenotypes's past year of commit activity
    Jupyter Notebook 0 MIT 0 1 1 Updated Nov 5, 2026
  • 2023-nematode-embryo-classifier Public
    Arcadia-Science/2023-nematode-embryo-classifier's past year of commit activity
    Python 0 MIT 0 0 2 Updated Nov 4, 2026
  • xanthate-lysis-gDNA-extraction Public

    Files, data, and analysis accompanying the forthcoming pub “A high-throughput method for genomic DNA extraction from Chlamydomonas.”

    Arcadia-Science/xanthate-lysis-gDNA-extraction's past year of commit activity
    Python 0 MIT 0 1 0 Updated Nov 4, 2026
  • sam3 Public Forked from facebookresearch/sam3

    The repository provides code for running inference and finetuning with the Meta Segment Anything Model 3 (SAM 3), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

    Arcadia-Science/sam3's past year of commit activity
    Python 0 1,867 0 1 Updated Nov 2, 2026
  • FPguide Public
    Arcadia-Science/FPguide's past year of commit activity
    Jupyter Notebook 0 MIT 0 1 4 Updated Nov 2, 2026
  • data-hub Public

    Data Hub makes lab instrument data instantly accessible to people, pipelines, and agents

    Arcadia-Science/data-hub's past year of commit activity
    TypeScript 16 MIT 3 0 0 Updated Nov 1, 2026
  • 2024-publishing-v2-early-assessment Public

    Data and code associated with "Early update on Arcadia publishing 2.0: Scientists are in charge, speed is an issue."

    Arcadia-Science/2024-publishing-v2-early-assessment's past year of commit activity
    Python 0 MIT 0 0 2 Updated Nov 1, 2026
  • menisquish-flat-agar Public

    A protocol for making flat agar and imaging C. elegans in 96-well plates

    Arcadia-Science/menisquish-flat-agar's past year of commit activity
    Jupyter Notebook 0 MIT 0 0 4 Updated Oct 31, 2026
  • crs-spectral-pipeline Public

    Pipeline for single-cell CRS spectral extraction: segmentation, tracking, and per-cell spectra from hyperspectral Raman microscopy data

    Arcadia-Science/crs-spectral-pipeline's past year of commit activity
    Python 0 MIT 0 0 7 Updated Oct 31, 2026
  • 2026-marine-broth-chlamy Public

    Image processing tools for fluorescence microscopy analysis of Chlamydomonas morphological transformations. Associated with "Marine Broth induces extreme morphological transformations in Chlamydomonas smithii"

    Arcadia-Science/2026-marine-broth-chlamy's past year of commit activity
    Jupyter Notebook 1 MIT 0 0 4 Updated Oct 31, 2026
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