imagej2

morphonets/SNT

The ImageJ framework for quantification of neuronal anatomy

DylanMuir/ReadImageJROI

Matlab function to import ROIs from ImageJ

tferr/Scripts

:microscope::cocktail: Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ

morphonets/cx3d

The Cx3D modeling framework in SciView and SNT

christianrickert/CU-CellSeg

Cell segmentation of multi-channel images

hadim/mm_scripts

A collection of scripts related to Micro-Manager.

berdal84/Mageek-Java

Mageek is an ImageJ Java plugin to batch process microscope images

christianrickert/CU-IScore

IHC scoring of multi-channel images

hilaprat/evm-imagej2

imcf/python-micrometa

:coffee: :snake: :microscope: Package for processing metadata from various light-microscopy related data formats.

BenjaminEscribano/PrairieDataManager

Prairie 2-Photon Microscopy Data Manager for recursive batch processing ans analysis with Fiji

christianrickert/CU-MacroLibrary

ImageJ2 macro library with variables and functions

fmeyenhofer/NanoZoomer-J

ImageJ plugin for handling NDPI files.

h39s/VessCoopJ

ImageJ Plugin for Automated Cancer Cell Vessel Co-option Analysis

imcf/jython-scijava-logging

:snake::coffee::bookmark_tabs: Jython package for using SciJava's LogService for logging.

jdebes/image-segmentation-imagej-plugin

ImageJ plugin containing a collection image segmentation algorithms.

ybajaj-29/StarDist_cmd

Command-line based, automatic image analysis pipeline to evaluate the bactericidal efficacy of polymer surface coatings against E. coli.

4QuantOSS/scijava-jupyter-kernel

Write SciJava scripts in Jupyter notebook!

imcf/jython-ome-model

:coffee: :snake: :microscope: :bookmark: :bookmark_tabs: A mavenized package of the Open Microscopy Environment "ome-model" Python module to be used in ImageJ2.

kmader/spark-scifio

A Spark-interface for the io.scif and other libraries to take advantage of the ImageJ2 ecosystem.