Pinned Repositories
fastem-sofima
Scable Optical Flow-based Image Alignment (SOFIMA) of FAST-EM datasets.
fastem-workflow
Post-processing software for FAST-EM data. Based on the iCAT-workflow by Ryan Lane.
iCAT-data
Partial dataset repository for iCAT-workflow.
iCAT-workflow
Post-processing workflow for integrated correlative array tomography (iCAT)
Kievits-FASTEM-array-tomography-2024
Lane-optimization-2020
Repository for the code, data, and analysis accompanying "Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy."
Mechanical-Analysis
Drift and vibration analysis of scanning electron microscope images
napari-psf-extractor
Point spread function extractor in napari
PSF-Extractor
Characterize the PSF of an optical setup
SF
Depth-dependent axial rescaling of 3D fluorescence microscopy data sets
hoogenboom-group's Repositories
hoogenboom-group/PSF-Extractor
Characterize the PSF of an optical setup
hoogenboom-group/SF
Depth-dependent axial rescaling of 3D fluorescence microscopy data sets
hoogenboom-group/iCAT-workflow
Post-processing workflow for integrated correlative array tomography (iCAT)
hoogenboom-group/fastem-workflow
Post-processing software for FAST-EM data. Based on the iCAT-workflow by Ryan Lane.
hoogenboom-group/Lane-optimization-2020
Repository for the code, data, and analysis accompanying "Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy."
hoogenboom-group/Mechanical-Analysis
Drift and vibration analysis of scanning electron microscope images
hoogenboom-group/napari-psf-extractor
Point spread function extractor in napari
hoogenboom-group/em-infrastructure
Documentation and configuration for Electron Microscopy server infrastructure
hoogenboom-group/fastem-sofima
Scable Optical Flow-based Image Alignment (SOFIMA) of FAST-EM datasets.
hoogenboom-group/iCAT-data
Partial dataset repository for iCAT-workflow.
hoogenboom-group/interactive-render-workflow
Interactive workflow for aligning volume electron microscopy datasets.
hoogenboom-group/Kievits-FASTEM-array-tomography-2024
hoogenboom-group/Kievits-OSTEM-2023
Code and analysis for publication titled "Optical STEM detection for scanning electron microscopy"
hoogenboom-group/catmaid-docker
Docker compose application for CATMAID
hoogenboom-group/focus-metrics
Functions to measure the focus level of fluorescence images
hoogenboom-group/mitonet-seg
MitoNet inference on Volume EM datasets
hoogenboom-group/q4STEM
hoogenboom-group/scripted-render-pipeline
automated pipeline interfacing with render-ws rest api
hoogenboom-group/secdetect
Small package for detecting tissue sections on ITO-coated glass