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    46 repositories

    • raman-analysis

      Public
      Spontaneous Raman analysis library
      Python
      •
      Other
      •1•1•2•4•Updated Feb 2, 2026Feb 2, 2026

    • integrator

      Public
      Proof of concept profile fitting and integration with neural nets
      HTML
      •0•3•0•0•Updated Jan 30, 2026Jan 30, 2026

    • yeast-mrcnn

      Public
      Another implementation of mask-rcnn for detecting budding yeast cells in microscopy images
      Python
      •
      MIT License
      •0•0•3•1•Updated Jan 5, 2026Jan 5, 2026

    • napari-labeller

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•1•1•Updated Jan 5, 2026Jan 5, 2026

    • microutil

      Public
      Python utils for working microscopy datasets
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•7•1•Updated Jan 5, 2026Jan 5, 2026

    • fast-overlap

      Public
      meep meep
      numpycythonopenmpopenmp-parallelization
      Python
      •2•0•2•1•Updated Jan 5, 2026Jan 5, 2026

    • valdo

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•13•2•Updated Dec 30, 2025Dec 30, 2025

    • SFcalculator_torch

      Public
      Differentiable pipeline connecting protein atomic models and scattering observables, both crystallography and cryoEM
      pytorch
      Python
      •
      MIT License
      •4•8•6•1•Updated Nov 20, 2025Nov 20, 2025

    • panel_mapper

      Public
      Map predicted reflection centroids to corresponding detector panel
      Python
      •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • dw

      Public
      jupyter notebooks exploring the double-Wilson model
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • dw-examples

      Public
      Examples of merging crystallographic intensities with a bivariate prior
      GLSL
      •0•0•2•0•Updated Sep 1, 2025Sep 1, 2025

    • marccd

      Public
      Read, write, and manipulate diffraction images that use the MarCCD format
      image-processingxray-diffractionxray-crystallography
      Python
      •
      MIT License
      •1•1•1•0•Updated Aug 16, 2025Aug 16, 2025

    • SFcalculator

      Public
      1•20•1•0•Updated Jul 16, 2025Jul 16, 2025

    • mdtools

      Public
      Tools for running MD simulations in OpenMM
      molecular-dynamicsopenmmmd-simulations
      Python
      •3•6•1•0•Updated Jun 24, 2025Jun 24, 2025

    • regroup

      Public
      Determine new space groups for analyzing pump-probe crystallography experiments
      Python
      •
      MIT License
      •1•1•0•0•Updated Mar 27, 2025Mar 27, 2025

    • SFcalculator_tf

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

    • SFcalculator_jax

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 20, 2025Jan 20, 2025

    • colav

      Public
      Calculate protein structural representations (dihedral angles, CA pairwise distances, and strain analysis) for downstream analysis (e.g., PCA, t-SNE, or UMAP).
      crystallographyprotein-dynamicsdrug-fragment
      Jupyter Notebook
      •
      MIT License
      •1•9•0•0•Updated Sep 11, 2024Sep 11, 2024

    • room-of-requirement

      Public
      Useful Lab Utilities
      Jupyter Notebook
      •1•0•1•0•Updated Jul 25, 2024Jul 25, 2024

    • Devices_Optics

      Public
      Code to collect and analyze data using the spectroscopic setup & data collected
      Jupyter Notebook
      •0•0•0•0•Updated Jun 6, 2024Jun 6, 2024

    • fasrc-ood-jupyter

      Public
      OnDemand app for serving Jupyter notebooks out of your local path
      HTML
      •
      MIT License
      •1•0•0•0•Updated May 27, 2024May 27, 2024

    • hadamuxer

      Public
      Demultiplex Hadamard-encoded diffraction images.
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 29, 2023Dec 29, 2023

    • scramble

      Public
      A tool for disambiguating serial laue data
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 15, 2023Nov 15, 2023

    • tape

      Public
      Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology…
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •133•0•0•0•Updated Nov 3, 2023Nov 3, 2023

    • cog

      Public
      Wrapper for Precognition to simplify Laue data reduction
      xray-diffractionxray-crystallographylaue
      Python
      •0•0•1•1•Updated Oct 17, 2023Oct 17, 2023

    • spectra-baseline

      Public
      Fast implementations of baseline subtraction for raman spectra
      Python
      •
      Other
      •0•0•1•2•Updated Oct 9, 2023Oct 9, 2023

    • russell-thesis

      Public
      Jupyter notebooks that were used for data analysis and figure making for John Russell's Ph.D. Thesis.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 23, 2023Jul 23, 2023

    • laue-index-assigner

      Public
      A robust algorithm for assigning miller indices to Laue data from approximate indexing solutions.
      Python
      •1•2•3•1•Updated Feb 17, 2023Feb 17, 2023

    • EF-X-crystal-MD

      Public
      Setup and analysis of MD simulations mimicking the application of an external electric field to a protein crystal.
      Jupyter Notebook
      •1•3•0•0•Updated Dec 21, 2022Dec 21, 2022

    • hekstra-lab.github.io

      Public
      Essentially a custom 404 in case anyone tries this URL
      HTML
      •0•0•0•0•Updated Nov 11, 2022Nov 11, 2022