Fiji

fiji

A "batteries-included" distribution of ImageJ :battery:

Trainable_Segmentation

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

Stitching

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

Auto_Threshold

fiji.github.io

Fiji website

Colocalisation_Analysis

Fiji's plugin for colocalization analysis

SPIM_Registration

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

3D_Viewer

register_virtual_stack_slices

Fiji package for registering and transforming arbitrarily large sequences of images

Fiji_Plugins

dockerfiles

Fiji Dockerfiles for Docker builds.

FilamentDetector

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

IO

LocalThickness

Descriptor_based_registration

fiji-builds

Downloadable Fiji bundles

H5J_Loader_Plugin

H5J Reader Plugin for Fiji project.

KymographBuilder

KymographBuilder is Yet Another Kymograph Fiji plugin.

simplified-io

Read, write, type convert images using simple methods.

CorrectBleach

Image_5D

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

learnathon-2019

Collection of material for the 2019 Learnathon

View5D

legacy-imglib1

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

Stochastic_Denoise

Volume_Viewer

blockmatching

CPU_Meter

learnathon-2017

Collection of tutorial repositories for 2017 DAIS learnathon

old-school-repls

Fiji's original script interpreter plugins