Repositories list

• iSIM

  Public
  iSIM control and analysis software

  Python

  •1•0•3•0•Updated Feb 26, 2026Feb 26, 2026

• just-focus

  Public
  Vector electromagnetic field calculations in the focus of high NA microscope objectives.

  Python

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Feb 2, 2026Feb 2, 2026

• qExM_code

  Public
  Data and code for Quantitative Expansion Microscopy for In Situ Estimation of Endogenous Target Abundance

  Python

  •0•0•0•0•Updated Jan 24, 2026Jan 24, 2026

• basic_training

  Public
  Resources for the basic training in microscopy course in the LEB

  microscopy

  C++

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 15, 2026Jan 15, 2026

• deep-events

  Public
  Scripts and notebooks for annotation and handling of phase and fluorescent data for preparation and training of neural networks for event detection.

  Python

  •

  GNU Affero General Public License v3.0

  •0•2•0•0•Updated Jan 12, 2026Jan 12, 2026

• pymmcore-eda

  Public
  Smart microscopy library at LEB EPFL

  Python

  •

  GNU Affero General Public License v3.0

  •0•2•0•0•Updated Jun 26, 2025Jun 26, 2025

• qExM_protocol

  Public
  Tutorials on how to do quantitative expansion microscopy sample preparation

  0•2•0•0•Updated Apr 2, 2025Apr 2, 2025

• napari-eda-highlight-reel

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•3•0•Updated Mar 7, 2025Mar 7, 2025

• Zeiss-microscope

  Public
  This is a wiki page for the labs Zeiss Axio Observer 7 microscope

  Python

  •0•2•2•0•Updated Mar 7, 2025Mar 7, 2025

• MitoSplit-Net

  Public
  Detection of mitochondrial divisions with neural networks

  Jupyter Notebook

  •

  Other

  •0•2•3•0•Updated Jan 6, 2025Jan 6, 2025

• ImageInjector

  Public
  A simple plugin for injecting images into Micro-Manager's demo camera.

  Java

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Nov 21, 2024Nov 21, 2024

• kpal

  Public
  Hardware control for imaging science

  Python

  •

  Other

  •0•1•0•0•Updated Oct 26, 2024Oct 26, 2024

• eda_plugin

  Public
  Plugin for event-driven acquisition to be used with Micro-Manager

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•5•0•0•Updated Jul 5, 2024Jul 5, 2024

• tracking-and-diffusion

  Public
  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Mar 8, 2024Mar 8, 2024

• ptycho

  Public
  Hardware control and image analysis code for Fourier ptychography.

  Jupyter Notebook

  •

  MIT License

  •0•4•0•0•Updated Jan 22, 2024Jan 22, 2024

• led-array-datasets

  Public
  0•0•0•0•Updated Oct 2, 2023Oct 2, 2023

• python-isim-control

  Public archive
  Python Control Interface for the iSIM at LEB-EPFL

  Python

  •

  GNU General Public License v3.0

  •0•0•1•0•Updated Aug 4, 2023Aug 4, 2023

• imajin

  Public archive
  Tools to simulate optics and microscopy experiments.

  Python

  •0•0•0•0•Updated Aug 3, 2023Aug 3, 2023

• project_layout

  Public template
  Python

  •0•2•0•0•Updated May 23, 2023May 23, 2023

• rats

  Public
  High performance probabilistic state machine simulator

  Rust

  •

  MIT License

  •0•0•0•0•Updated Mar 16, 2023Mar 16, 2023

• eda-napari

  Public
  event-driven-acquisition plugin for napari

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•2•0•Updated Feb 2, 2023Feb 2, 2023

• pymm-eventserver

  Public
  Event Server to receive Micro-Manager events in python via zeromq

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Dec 7, 2022Dec 7, 2022

• EDA

  Public
  Tools for adaptive imaging in the LEB-EPFL

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•3•0•0•Updated Aug 19, 2022Aug 19, 2022

• WGmode

  Public
  2D simulation functions for slab and ridge waveguide mode study

  MATLAB

  •3•4•0•0•Updated Oct 30, 2018Oct 30, 2018

• StormChaser

  Public
  DEMO 3D Double-Helix localization software

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 29, 2018Aug 29, 2018

• ALICA

  Public
  Automated Laser Illumination Control Algorithms

  Java

  •

  GNU General Public License v3.0

  •3•6•2•0•Updated Jul 13, 2018Jul 13, 2018

• mm-docker

  Public
  Dockerfiles for building Micro-Manager components.

  Shell

  •

  GNU General Public License v3.0

  •0•2•1•0•Updated Jun 13, 2018Jun 13, 2018

• ALICA_ACPack

  Public
  Analyzer and controller implementations for ALICA.

  Java

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Jun 6, 2018Jun 6, 2018

• SASS

  Public
  Toolkit for simulating real-time control systems for super-resolution microscopy.

  stormimagejsimulation+ 3microscopysuper-resolutionpalm

  Java

  •

  GNU General Public License v3.0

  •4•7•7•0•Updated Jun 5, 2018Jun 5, 2018

• DEFCoN-ImageJ

  Public
  An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks.

  imagejfijifluorescence+ 1microscopy

  Java

  •

  GNU General Public License v3.0

  •0•2•2•0•Updated Jun 5, 2018Jun 5, 2018