ImageJ 2.0.0 rc71 – Image Processing & Analysis in Java

ImageJ 2.0.0 rc71

:: DESCRIPTION

ImageJ is a public domain Java image processing program.ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.

::DEVELOPER

ImageJ team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

ImageJ

:: MORE INFORMATION

Citation:

Abramoff, M.D., Magelhaes, P.J., Ram, S.J. “Image Processing with ImageJ“.
Biophotonics International, volume 11, issue 7, pp. 36-42, 2004.

MorphoLibJ 1.2.2 – Collection of Mathematical Morphology Methods and Plugins for ImageJ

MorphoLibJ 1.2.2

:: DESCRIPTION

The MorphoLibJ library proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins.

::DEVELOPER

IJPB Modeling and digital imaging lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 MorphoLibJ

:: MORE INFORMATION

Citation

MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ.
Legland D, Arganda-Carreras I, Andrey P.
Bioinformatics. 2016 Jul 13. pii: btw413.

Fiji 20141125 – Image Processing Package based on ImageJ

Fiji 20141125

:: DESCRIPTION

Fiji (Fiji is Just ImageJ) is an image processing package. It can be described as a distribution of ImageJ together with Java, Java 3D and a lot of plugins organized into a coherent menu structure.

::DEVELOPER

Fiji Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Fiji

:: MORE INFORMATION

Publications introducing Fiji

ThunderSTORM 1.3 – ImageJ plugin for PALM and STORM data analysis and super-resolution imaging

ThunderSTORM 1.3

:: DESCRIPTION

ThunderSTORM is an open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy.

::DEVELOPER

Institute of Cellular Biology and PathologyFirst Faculty of MedicineCharles University in Prague, Czech Republic.

:: SCREENSHOTS

ThunderSTORM

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 ThunderSTORM

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 25. pii: btu202. [Epub ahead of print]
ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging.
Ovesný M, Křížek P, Borkovec J, Svindrych Z, Hagen GM.

microManager 1.4.21 – ImageJ Plugin of Imaging & Control of Automated Microscopes

microManager 1.4.21

:: DESCRIPTION

microManager (also called μManager) is a ImageJ Plugin for control of automated microscopes. It lets you execute common microscope image acquisition strategies such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. μManager works with microscopes from all four major manufacturers (Leica, Nikon, Olympus and Zeiss), most scientific-grade cameras and many peripherals (stages, filter wheels, shutters, etc.) used in microscope imaging.

::DEVELOPER

Vale Lab, UCSF

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

microManager

:: MORE INFORMATION

Curr Protoc Mol Biol. 2010 Oct;Chapter 14:Unit14.20. doi: 10.1002/0471142727.mb1420s92.
Computer control of microscopes using µManager.
Edelstein A, Amodaj N, Hoover K, Vale R, Stuurman N.

BDML4DViewer 0.20 – Plugin of ImageJ software for Visalizing BDML files

BDML4DViewer 0.20

:: DESCRIPTION

BDML4DViewer is a pulugin of ImageJ software. The plugin enables reading and visualizing content of BDML files

::DEVELOPER

The Systems Science of Biological Dynamics (SSBD) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BDML4DViewer

:: MORE INFORMATION

MOSAIC 201305 – ImageJ plugin for Biological Fluorescence Microscopy

MOSAIC 201305

:: DESCRIPTION

MOSAIC (MOdels, Simulations, and Algorithms for Interdisciplinary Computing) , the image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy , are available as plugins for the popular free image processing software ImageJ.

::DEVELOPER

MOSAIC group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MOSAIC

:: MORE INFORMATION

Citation:

I. F. Sbalzarini and P. Koumoutsakos.
Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology,
Journal of Structural Biology 151(2):182-195, 2005.

ITCN 1.6 – ImageJ Plugin for Image-based Tool for Counting Nuclei

ITCN 1.6

:: DESCRIPTION

ITCN (Image-based Tool for Counting Nuclei) is an ImageJ plugin for counting the number cells within an image. The inputs are:

  1. an estimation of the diameter of a cell
  2. an estimation of the minimum distance between cells
  3. either a region of interest (ROI) selected with ImageJ’s selection tools or a black and white mask image that is white in regions that are to be counted

::DEVELOPER

The Center for Bio-Image Informatics

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

ITCN

:: MORE INFORMATION

Download itcn_.jar to the plugins folder of ImageJ and restart ImageJ.

BQBisqueJ 0.1 – ImageJ plugin for Bisque DataBase System

BQBisqueJ 0.1

:: DESCRIPTION

BQBisqueJ is an ImageJ plugin that allows direct access to the Bisque DataBase system.

::DEVELOPER

The Center for Bio-Image Informatics

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BQBisqueJ ; Source Code

:: MORE INFORMATION

BQBisqueJ requires adding a Bisque JAR file to ImageJ. In ImageJ 1.31 or later, this is done by copying the Bisque JAR file into the plugins folder or an immediate subfolder of the plugins folder, then restarting ImageJ.

Costanza 1.0 – ImageJ Plugin for Image Segmentation & Analyzing Stacks

Costanza 1.0

:: DESCRIPTION

Costanza (COnfocal STack ANalyZer Application) is a Image segmentation software developed for 3D confocal data. Implemented in Java as a plugin to ImageJ.

Costanza is used to segment compartments (cells) in a stack and to extract quantitative data for the extracted compartments, including intensities from a second stack.

::DEVELOPER

Michael Green, Pawel Krupinski, Pontus Melke, Patrik Sahlin, Henrik Jönsson
Computational Biology & Biological Physics, Lund University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Costanza ; userguide.pdf.

:: MORE INFORMATION

Source code is available upon request (henrik at thep.lu.se).