Discover fiji/FlowJ Open Source project by Fiji (@fiji)

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Java
License
GNU General Publi...
Created over 10 years ago
Updated over 2 years ago

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Plugins from Biomedical Imaging in Java (BIJ)

fiji

A "batteries-included" distribution of ImageJ 🔋

Shell

767

Trainable_Segmentation

Fiji library to perform image segmentation based on the Weka learning schemes

Java

111

Stitching

Fiji's Stitching plugins reconstruct big images from tiled input images.

Auto_Threshold

fiji.github.io

AnalyzeSkeleton

ImageJ/Fiji plugin to analyze 2D and 3D skeleton images

Java

Colocalisation_Analysis

Fiji's plugin for colocalization analysis

Java

cookbook

Plugins collated for the Fiji Cookbook

Java

SPIM_Registration

Deprecated, instead check out: https://github.com/preibischLab/multiview-reconstruction & https://github.com/PreibischLab/BigStitcher

Java

bUnwarpJ

ImageJ/Fiji plugin for consistent elastic registration of 2D images

Java

3D_Viewer

Java

register_virtual_stack_slices

Fiji package for registering and transforming arbitrarily large sequences of images

Java

microscope-image-quality

TensorFlow-based classifier for microscope image focus quality.

Java

Skeletonize3D

ImageJ/Fiji plugin to skeletonize binary images

javac

VIB

Fiji_Plugins

SNT

Legacy project superseded by https://github.com/morphonets/SNT

Java

Jama

OBSOLETE; see http://central.maven.org/maven2/gov/nist/math/jama/1.0.3/

Java

HDF5_Vibez

HDF5 plugin for ImageJ and Fiji.

Java

Graph_Cut

Java

dockerfiles

Fiji Dockerfiles for Docker builds.

Dockerfile

Kappa

A Fiji plugin for Curvature Analysis

Jupyter Notebook

Java

FilamentDetector

A Fiji plugin that allows easy, fast and accurate detection and tracking of biological filaments.

Java

LocalThickness

Java

Directionality

A Fiji plugin for inferring the main orientation of structures in an image.

Java

fiji-builds

Downloadable Fiji bundles

Shell

Correct_3D_Drift

Python

VIB-lib

Java

Descriptor_based_registration

Java

level_sets

Java

OMEVisual

A Fiji plugin to easily visualize OME metadata.

Java

Siox_Segmentation

Fiji plugin based on the SIOX project to segment color images

Java

MTrack2

Java

Colour_Deconvolution

Java

pom-fiji

OBSOLETE - Use https://github.com/scijava/pom-scijava instead!

pQCT

Fiji plugins for pQCT image analysis.

Java

CorrectBleach

Java

H5J_Loader_Plugin

H5J Reader Plugin for Fiji project.

Java

KymographBuilder

KymographBuilder is Yet Another Kymograph Fiji plugin.

Java

simplified-io

Read, write, type convert images using simple methods.

Java

IJ_Robot

This plugin calls the Robot Java class. The purpose of the plugin is to allow the macro language to control other programs via clicking and key presses.

Java

BalloonSegmentation

Java

Image_5D

A plugin to extend image stacks to 5 dimensions: x, y, channel (color), slice (z), frame (t).

Volume_Calculator

Cell_Counter

Dichromacy

fiji-compat

[OBSOLETE] Merged with fiji/fiji

Kuwahara_Filter

Auto_Local_Threshold

Vaa3d_Reader

SplineDeformationGenerator

3D_Blob_Segmentation

View5D

3D_Objects_Counter

learnathon-2019

Collection of material for the 2019 Learnathon

Java

panorama

Java

Feature_Detection

Java

JMathLib

Mirror of JMathLib project

Java

Stochastic_Denoise

Java

Color_Histogram

Java

Interactive_3D_Surface_Plot

Series_Labeler

LSM_Reader

PIV_analyser

Color_Inspector_3D

ToAST

Multi_Kymograph

Statistical_Region_Merging

Java

Manual_Tracking

Java

Time_Lapse

A set of tools intended to help with time-lapse data

Java

Volume_Viewer

Java

Stack_Manipulation

Java

legacy-imglib1

OBSOLETE; see https://github.com/imglib/imglib2

Java

Threshold_Colour

OBSOLETE; included with https://github.com/imagej/imagej1

QuickPALM

Time_Stamper

fiji-lib

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

FS_Align_TrakEM2

registration_3d

Lasso_and_Blow_Tool

fiji/FlowJ

fiji

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