Java

Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences. It is a free, open-source, community-driven project.

OMERO is a free, open source image management software. It is client-server based system which supports 5D images, including big images and high-content screening data. Data are stored on a server using relational database. They are accessed using 3 main clients, a desktop client, a web client and a command line tool. There are bindings from OMERO to other image analysis packages, like FLIMfit, OMERO.searcher. The data in OMERO are organized in groups. A user can be a member of one or more groups. This groups can be collaborative or private, there are 4 levels of permissions to access/edit/annotate/delete the data of other users.

The package is supported not only by community forums, but also by a dedicated team which helps users to solve their problems and deals with the bugs submitted via error submission system.

###Strengths

Open source, scalable software, Supports diverse sets of imaging applications and domains (EM,LM, HCS, DigPath) Cross-platform, Java-based application, API support for Java, Python, C++, Django, On-line Forums, Automatic QA and upload of software errors Multi-dimensional images, Web access, Free Demo-server accounts

Limitations

Enterprise-scale software, so complex install, requires expertise, Actively developing API, Python scripts and functions still developing

‘’’Squassh’’’ is a tool for 2D and 3D segmentation and quantification of subcellular shapes in fluorescence microscopy images. It provides globally optimal detection and segmentation of objects with constant internal intensity distribution, followed by object-based colocalization analysis. The segmentation computed by Region Competition can optionally correct for the PSF of the microscope, hence providing optimally deconvolved segmentations. Part of the mosaic suite

quote:

This plugin allows to apply a free affine transformation to a 2D image in an interactive way.

The purpose of this plugin is to register—in other words, to align or to match—two images, one of them being called the source image and the other the target image.