Repositories list

• RS-FISH-Spark

  Public
  Spark version of RS-FISH that can analyze large N5 volumes in a distributed fashion locally, on the cluster or in the cloud

  Java

  •

  GNU General Public License v2.0

  •1•8•1•2•Updated Sep 6, 2025Sep 6, 2025

• STIM

  Public
  Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.

  Java

  •

  GNU General Public License v3.0

  •1•31•2•0•Updated May 27, 2025May 27, 2025

• RS-FISH

  Public
  Tool for precise, interactive, fast and scalable FISH spot detection

  Java

  •

  GNU General Public License v2.0

  •15•50•10•0•Updated Feb 4, 2025Feb 4, 2025

• FunctionFit

  Public
  Extension of Saalfelds mpi-cbg package for function fits

  Java

  •

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

  •1•2•0•0•Updated Feb 4, 2025Feb 4, 2025

• Drosophila_Single_Cell_Brain_Circadian

  Public
  Java

  •0•0•0•3•Updated Oct 3, 2024Oct 3, 2024

• FRC-QE

  Public
  Fourier Ring Correlation-based estimation of clearing quality

  HTML

  •2•6•0•0•Updated Jul 13, 2023Jul 13, 2023

• PINNA-2D

  Public
  PINNA 2D - Pixel-wIse NeuroN Annotation

  Kotlin

  •0•0•0•1•Updated May 23, 2023May 23, 2023

• bigdataviewer-core-movie

  Public
  ImgLib2-based viewer for registered SPIM stacks and more

  Java

  •

  BSD 2-Clause "Simplified" License

  •39•3•0•0•Updated Nov 28, 2022Nov 28, 2022

• nd2totif-maskembryos-stagebin-pipeline

  Public
  embryo images python pipeline

  Python

  •1•1•0•0•Updated Nov 10, 2022Nov 10, 2022

• multiview-simulation

  Public
  Code for simulating a multi-view acquisition including attenuation, convolution, reduced sampling and poission noise

  Java

  •

  GNU General Public License v2.0

  •5•13•0•0•Updated Jun 14, 2022Jun 14, 2022

• preibisch-labsite

  Public
  Lab's website

  HTML

  •0•0•0•0•Updated Jul 21, 2021Jul 21, 2021

• wing-landmark-detection-CNN

  Public
  Drosophila wing CNN for landmark detection

  Jupyter Notebook

  •0•1•0•0•Updated Mar 28, 2021Mar 28, 2021

• worm-straightening

  Public
  Stretch worms to register to same space

  Python

  •0•0•0•0•Updated Mar 26, 2021Mar 26, 2021

• image_RF

  Public
  Image analysis random forest classifier

  Python

  •0•0•0•0•Updated Mar 7, 2021Mar 7, 2021

• segmentation_viterbi

  Public
  Approach used for nuclei segmentation of the dauer EM

  MATLAB

  •0•0•0•0•Updated Feb 27, 2021Feb 27, 2021

• PixelWise_Cell_Classification

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 22, 2020Sep 22, 2020

• annotation_plugin

  Public
  Java

  •0•0•0•0•Updated Apr 30, 2020Apr 30, 2020

• pretty-graphs

  Public
  Contains the notebooks to plot the smFISH histograms

  Jupyter Notebook

  •0•1•0•0•Updated Apr 8, 2020Apr 8, 2020

• BigStitcher-Singularity

  Public
  Singularity container description for BigStitcher

  Shell

  •0•0•0•0•Updated Mar 19, 2020Mar 19, 2020

• mvrecon

  Public
  refactoring multi view reconstruction

  Java

  •0•0•0•0•Updated Jan 20, 2020Jan 20, 2020

• ImageJmacro

  Public
  Set of macro for ImageJ

  0•0•0•0•Updated Dec 4, 2019Dec 4, 2019

• Spark-Test

  Public
  Playing with Spark

  Java

  •0•0•0•0•Updated Oct 16, 2019Oct 16, 2019

• RemoveUnconnectedGraph

  Public
  Semiautomatically "track" the junctions on a binary image

  Java

  •0•1•0•0•Updated Aug 20, 2019Aug 20, 2019

• snake-microscopy

  Public
  Active Contour for microscopy image Matlab implementation - Kass, Greedy, GVF

  MATLAB

  •0•1•0•0•Updated Jul 1, 2019Jul 1, 2019

• bigstitcher-paper

  Public
  text and ressources for the BigStitcher publication

  TeX

  •0•0•0•0•Updated Jun 4, 2019Jun 4, 2019

• bigstitcher-benchmark

  Public
  Code for assessing the quality of BigStitcher registration on simulated data

  Jupyter Notebook

  •0•0•0•0•Updated Apr 16, 2019Apr 16, 2019

• WormFit

  Public
  software for segmentation and analysis of smFISH worm images

  Java

  •0•0•0•0•Updated Jul 30, 2018Jul 30, 2018

• cell-counting-zebrafish

  Public
  Shell

  •0•1•0•0•Updated Jun 12, 2018Jun 12, 2018

• EmbryoMatching

  Public
  Find corresponding embryos imaged with confocal/epifluoresence

  Java

  •0•0•0•0•Updated Feb 20, 2018Feb 20, 2018

• embryo-lineages

  Public
  Tracking of the C. elegans embryo development using MaMuT

  Java

  •11•1•0•0•Updated Jan 16, 2018Jan 16, 2018