PreibischLab

BigStitcher

ImgLib2/BDV implementation of Stitching for large datasets

RS-FISH

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

multiview-reconstruction

Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data

STIM

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

multiview-simulation

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

RS-FISH-Spark

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

FRC-QE

Fourier Ring Correlation-based estimation of clearing quality

bigdataviewer-core-movie

ImgLib2-based viewer for registered SPIM stacks and more

cell-counting-zebrafish

FunctionFit

Extension of Saalfelds mpi-cbg package for function fits

nd2totif-maskembryos-stagebin-pipeline

embryo images python pipeline

pretty-graphs

Contains the notebooks to plot the smFISH histograms

RemoveUnconnectedGraph

Semiautomatically "track" the junctions on a binary image

snake-microscopy

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

wing-landmark-detection-CNN

Drosophila wing CNN for landmark detection

ImageJmacro

Set of macro for ImageJ

preibisch-labsite

Lab's website

annotation_plugin

bigstitcher-benchmark

Code for assessing the quality of BigStitcher registration on simulated data

bigstitcher-paper

text and ressources for the BigStitcher publication

BigStitcher-Singularity

Singularity container description for BigStitcher

Drosophila_Single_Cell_Brain_Circadian

image_RF

Image analysis random forest classifier

mvrecon

refactoring multi view reconstruction

PINNA-2D

PINNA 2D - Pixel-wIse NeuroN Annotation

PixelWise_Cell_Classification

segmentation_viterbi

Approach used for nuclei segmentation of the dauer EM

Spark-Test

Playing with Spark

worm-straightening

Stretch worms to register to same space

WormFit

software for segmentation and analysis of smFISH worm images