Repositories list

• tpx3HitParser

  Public
  Parse Timepix3 raw files to hits, clusters and events

  Python

  •1•12•0•1•Updated Jun 15, 2023Jun 15, 2023

• tpx3EventViewer

  Public
  Convert the sparse event stream (in HDF5) from tpx3HitParser to frames

  Python

  •

  MIT License

  •0•1•0•0•Updated Mar 13, 2023Mar 13, 2023

• mtf-nps-dqe

  Public
  Python scripts for measuring MTF and NPS, and calculating DQE.

  npscryo-emdetectors+ 3mtfdqepython

  Python

  •

  MIT License

  •0•2•0•0•Updated Jul 20, 2022Jul 20, 2022

• InSilicoTEM

  Public
  Simulator of a Transmission Electron Microscope (TEM) optimized for biological specimen.

  MATLAB

  •4•10•2•0•Updated Dec 13, 2021Dec 13, 2021

• 4k-screen

  Public
  Scripts to run the 4k screen

  Python

  •0•0•0•0•Updated Sep 14, 2021Sep 14, 2021

• relion

  Public
  Image-processing software for cryo-electron microscopy

  C++

  •

  Other

  •202•0•0•0•Updated Sep 2, 2021Sep 2, 2021

• tpx3-event-localisation

  Public
  Sub-pixel electron detection using a convolutional neural network

  Python

  •

  MIT License

  •0•2•0•0•Updated Aug 12, 2020Aug 12, 2020

• omero-user-scripts

  Public
  Plugins for OMERO

  Python

  •

  GNU General Public License v2.0

  •52•0•0•0•Updated May 25, 2020May 25, 2020

• bioformats

  Public
  Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

  Java

  •

  GNU General Public License v2.0

  •242•1•0•0•Updated Apr 3, 2020Apr 3, 2020

• geant4medipix

  Public
  Pixel based Medipix geometry with digitiser for simulating Monte Carlo and charge transport simulation as well as chip electronics.

  C++

  •

  MIT License

  •6•4•1•0•Updated Mar 2, 2020Mar 2, 2020

• tpx3-tot-correction

  Public
  Matlab scripts to calculate the ToT correction matrix

  MATLAB

  •0•0•0•0•Updated Feb 5, 2020Feb 5, 2020

• instamatic

  Public
  Python program to collect serial and rotation electron diffraction data

  Python

  •

  GNU General Public License v3.0

  •28•0•0•0•Updated Sep 12, 2019Sep 12, 2019

• sd-auto-copier

  Public
  Python application intended to run on RasberryPi to automatically read an SD card and copy its contents to the network drive

  Python

  •0•0•0•0•Updated Feb 1, 2019Feb 1, 2019

• focus

  Public
  High Throughput Electron Microscopy Image Processing Software

  C++

  •

  GNU General Public License v2.0

  •14•0•0•0•Updated Oct 17, 2018Oct 17, 2018

• trajectory-model

  Public
  C++

  •0•0•0•0•Updated Sep 4, 2017Sep 4, 2017

• openmicroscopy

  Public
  OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded …

  Java

  •

  GNU General Public License v2.0

  •102•0•0•0•Updated Jun 16, 2016Jun 16, 2016

• linescan

  Public
  MATLAB

  •0•0•0•0•Updated May 17, 2016May 17, 2016

• motioncorr

  Public
  motion correction for movies recorded using direct electron detectors

  C++

  •8•0•0•0•Updated Apr 26, 2016Apr 26, 2016

• ome-documentation

  Public
  Sphinx-based documentation for the Open Microscopy Environment

  Shell

  •51•0•0•0•Updated Jan 18, 2016Jan 18, 2016