PreibischLab's repositories
BigStitcher
ImgLib2/BDV implementation of Stitching for large datasets
multiview-reconstruction
Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data
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
FunctionFit
Extension of Saalfelds mpi-cbg package for function fits
PINNA-2D
PINNA 2D - Pixel-wIse NeuroN Annotation
bigdataviewer-core-movie
ImgLib2-based viewer for registered SPIM stacks and more
nd2totif-maskembryos-stagebin-pipeline
embryo images python pipeline
multiview-simulation
Code for simulating a multi-view acquisition including attenuation, convolution, reduced sampling and poission noise
preibisch-labsite
Lab's website
wing-landmark-detection-CNN
Drosophila wing CNN for landmark detection
worm-straightening
Stretch worms to register to same space
image_RF
Image analysis random forest classifier
segmentation_viterbi
Approach used for nuclei segmentation of the dauer EM
pretty-graphs
Contains the notebooks to plot the smFISH histograms
BigStitcher-Singularity
Singularity container description for BigStitcher
mvrecon
refactoring multi view reconstruction
ImageJmacro
Set of macro for ImageJ
Spark-Test
Playing with Spark
RemoveUnconnectedGraph
Semiautomatically "track" the junctions on a binary image
snake-microscopy
Active Contour for microscopy image Matlab implementation - Kass, Greedy, GVF
bigstitcher-paper
text and ressources for the BigStitcher publication
bigstitcher-benchmark
Code for assessing the quality of BigStitcher registration on simulated data
WormFit
software for segmentation and analysis of smFISH worm images