2D

Estimate the frequency of hepatitis C virus infected cells based on the intensity of viral antigen associated immunofluorescence. 

The core is an ImageJ Macro, so it's easy to modify for one's own needs (Link to the code). 

XuvTools (pronounced “ex-you-vee-tools”) is a fully automated 3D stitching software for biomedical image data, typically confocal microscopy images. XuvTools runs on Microsoft Windows XP and Vista, Linux and Apple Mac computers. It supports 32 and 64bit operating systems (with 64bit highly preferred). XuvTools is free and open source software (see Licensing), so you can start using it immediately. Go to Downloads and give it a try. The goal of XuvTools is to provide tools, that combine multiple microscopic recordings to obtain a larger field of view (“stitching”) and a higher dynamic range (“HDR” recombination), or better resolution (multi view reconstruction), and to make these tools publicly available.

The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.

Auto-Bayes is a software package based on Bayesian statistics and requires no user dependent parameters for molecule detection and image reconstruction for Single-Molecule Localization Microscopy (SMLM), including photoactivated localization microscope (PALM), stochastic optical reconstruction microscope (STORM), and direct stochastic optical reconstruction microscopy (dSTORM), etc.

This software is designed for the rapid semi-automatic detection and quantification of synaptic protein puncta from 2D immunofluorescence images generated by confocal laser scanning microscopy.