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    19 repositories

    • scripted-render-pipeline

      Public
      automated pipeline interfacing with render-ws rest api
      Python
      •
      GNU General Public License v3.0
      •0•0•7•1•Updated Nov 15, 2024Nov 15, 2024

    • fastem-sofima

      Public
      Scable Optical Flow-based Image Alignment (SOFIMA) of FAST-EM datasets.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

    • em-infrastructure

      Public
      Documentation and configuration for Electron Microscopy server infrastructure
      Shell
      •
      MIT License
      •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • catmaid-docker

      Public
      Docker compose application for CATMAID
      Shell
      •3•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • Kievits-OSTEM-2023

      Public
      Code and analysis for publication titled "Optical STEM detection for scanning electron microscopy"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 24, 2024Sep 24, 2024

    • interactive-render-workflow

      Public
      Interactive workflow for aligning volume electron microscopy datasets.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•4•0•Updated Sep 3, 2024Sep 3, 2024

    • mitonet-seg

      Public
      MitoNet inference on Volume EM datasets
      Python
      •
      Other
      •0•0•2•0•Updated Jul 4, 2024Jul 4, 2024

    • Kievits-FASTEM-array-tomography-2024

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 4, 2024Jul 4, 2024

    • iCAT-workflow

      Public
      Post-processing workflow for integrated correlative array tomography (iCAT)
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•2•3•0•Updated Jun 7, 2024Jun 7, 2024

    • SF

      Public
      Depth-dependent axial rescaling of 3D fluorescence microscopy data sets
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •1•4•0•0•Updated Jun 1, 2024Jun 1, 2024

    • PSF-Extractor

      Public
      Characterize the PSF of an optical setup
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•8•3•0•Updated May 7, 2024May 7, 2024

    • napari-psf-extractor

      Public
      Point spread function extractor in napari
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 26, 2023Dec 26, 2023

    • q4STEM

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 12, 2023Apr 12, 2023

    • fastem-workflow

      Public
      Post-processing software for FAST-EM data. Based on the iCAT-workflow by Ryan Lane.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 2, 2023Mar 2, 2023

    • Mechanical-Analysis

      Public
      Drift and vibration analysis of scanning electron microscope images
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•1•0•0•Updated Sep 29, 2022Sep 29, 2022

    • focus-metrics

      Public
      Functions to measure the focus level of fluorescence images
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 14, 2022Jun 14, 2022

    • iCAT-data

      Public
      Partial dataset repository for iCAT-workflow.
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Apr 29, 2022Apr 29, 2022

    • secdetect

      Public
      Small package for detecting tissue sections on ITO-coated glass
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 10, 2022Mar 10, 2022

    • Lane-optimization-2020

      Public
      Repository for the code, data, and analysis accompanying "Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy."
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•1•0•0•Updated Feb 23, 2022Feb 23, 2022