Fiji

A "batteries included" distribution of ImageJ for scientific image analysis

Pinned Repositories

AnalyzeSkeleton
ImageJ/Fiji plugin to analyze 2D and 3D skeleton images
Language:Java26 17 821
Auto_Threshold
Language:Java42 20 330
bUnwarpJ
ImageJ/Fiji plugin for consistent elastic registration of 2D images
Language:Java23 17 1310
Colocalisation_Analysis
Fiji's plugin for colocalization analysis
Language:Java26 19 5617
cookbook
Plugins collated for the Fiji Cookbook
Language:Java25 20 85
fiji
A "batteries-included" distribution of ImageJ :battery:
Language:Shell786 53 273237
fiji.github.io
Fiji website
Language:HTML35 24 1011
SPIM_Registration
Deprecated, instead check out: https://github.com/preibischLab/multiview-reconstruction & https://github.com/PreibischLab/BigStitcher
Language:Java23 23 9922
Stitching
Fiji's Stitching plugins reconstruct big images from tiled input images.
Language:Java97 21 5764
Trainable_Segmentation
Fiji library to perform image segmentation based on the Weka learning schemes
Language:Java113 23 5561

Fiji's Repositories

fiji/Auto_Threshold
Language:Java42 20 330
fiji/cookbook
Plugins collated for the Fiji Cookbook
Language:Java25 20 85
fiji/bUnwarpJ
ImageJ/Fiji plugin for consistent elastic registration of 2D images
Language:Java23 17 1310
fiji/register_virtual_stack_slices
Fiji package for registering and transforming arbitrarily large sequences of images
Language:Java18 9 1312
fiji/microscope-image-quality
TensorFlow-based classifier for microscope image focus quality.
Language:Java17 13 62
fiji/Kappa
A Fiji plugin for Curvature Analysis
Language:Jupyter Notebook7 6 131
fiji/FilamentDetector
A Fiji plugin that allows easy, fast and accurate detection and tracking of biological filaments.
Language:Java6 3 182
fiji/fiji-builds
Downloadable Fiji bundles
Language:Shell5 9 63
fiji/H5J_Loader_Plugin
H5J Reader Plugin for Fiji project.
Language:Java4 16 13
fiji/level_sets
Language:Java4 16 03
fiji/OMEVisual
A Fiji plugin to easily visualize OME metadata.
Language:Java4 5 31
fiji/VIB-lib
Language:Java4 14 129
fiji/KymographBuilder
KymographBuilder is Yet Another Kymograph Fiji plugin.
Language:Java3 4 124
fiji/pQCT
Fiji plugins for pQCT image analysis.
Language:Java3 8 05
fiji/panorama
Language:Java2 15 14
fiji/Vaa3d_Reader
Language:Java2 15 01
fiji/Feature_Detection
Language:Java1 14 15
fiji/fiji-lib
Language:Java1 15 03
fiji/FS_Align_TrakEM2
Language:Java1 9 01
fiji/registration_3d
Language:Java1 15 11
fiji/weave_jy2java
A framework for inlining java code in an otherwise interpreted programming language running on the JVM, such as jython. See https://github.com/fiji/fiji/issues/161
Language:Java1 7 2
fiji/.github
Fiji organization profile
6 0
fiji/bij
Bio-medical imaging in Java
Language:Java15 11
fiji/Fiji_Developer
Language:Java16 01
fiji/pal-optimization
Language:Java
fiji/Reconstruct_Reader
Language:Java8 0
fiji/TopoJ
Language:Java15 02
fiji/TrakEM2_Archipelago
Language:Java8 0
fiji/Vaa3d_Writer
Vaa3d writer plugin for ImageJ 1.x
Language:Java16 0
fiji/Video_Editing
Language:Java1