LOCI Software Overview

The Data Browser is an ImageJ plugin that facilitates quick browsing of multichannel, multi-focal plane time course datasets. It is integrated with the Bio-Formats importer plugin—as well as ImageJ's built-in hyperstack and virtual stack support—to provide multidimensional visualization capabilities across space, time and channels.

The Fusion Event Locator & Classifier is an ImageJ macro & MATLAB function to identify fusion events in image stack & classify as proliferating or unchanging.

Jar2Lib is a command line tool for generating C++ proxy classes corresponding to a Java library. We use it to generate the BF-CPP bindings for our Bio-Formats library.

The SLIM Plotter is a tool for interactive visualization and inspection of combined spectral lifetime (SLIM) data. It was originally developed for internal use within LOCI and the White and Keely labs, but has grown into an application that may be useful to others as well.

Threshold and Calculate Average Intensity with Brush tools Macro is customized for immunohistochemistry image analysis done in the Ogle Lab.  It is especially suited for stained tissue sections that have large areas of background interspersed between areas of signal. 

As part of the development of ImageJ2, we are reworking VisBio as a collection of ImageJ plugins. There is an initial version of one such plugin, VisBio Ortho Stack, available as part of the LOCI Fiji plugins.

WiscScan Flow Cytometry is a standalone tool for flow cytometry analysis. It works as a plugin for ImageJ that enables post-acquisition analysis of flow cytometry data.