is the data acquisition and analysis program from BD Bioscience and operates in the Macintosh environment on the FACSCalibur cytometers.

  • CellQuest Acquistion Tutorial
  • CellQuest Analysis Tutorial
  • CellQuest Users Guide
  • Vendor WebSite


is BD Bioscience's next generation data acquisition and analysis program and operates in the PC Windows environment on the FACSAria, FACSCanto, LSRII and Fortessa.

  • Getting Started with BD FACSDiva Software
  • FACSDiVa Video Tutorial
  • FACSiVa Reference Manual
  • Vendor WebSite

Imaging Software:


is the software package used to analyze ImageStream data. Since efficient ImageStream data analysis demands ample computer storage space, powerful processing speed, and fast network connections, dedicated 64 bit, dual quad core workstations with 24GB of RAM and gigabit network connections are set-up at the facility. There are 4 workstations and access to them is free of charge and (as of yet) there is no need for reservations. The software has options to export calculated image features in .fcs format which can be read by conventional flow cytometry software and also has options to export analysis statistics in .txt format for import into graphing programs. In addition to support provided by the facility, the vendor also provides supports to registered users. Registration is free and is available at https://www.amnis.com/register.html

Image Pro Plus 6.3

is a software package for advanced image analysis. It accepts a wide variety of image file formats. The software is installed on all imaging work stations in the facility but since we only have one license which is controlled by a dongle it will only work on 1 station at a time.

Leica AF

is the software package that enables image capture and image analysis of files captured by the Leica SP2 confocal microscope and the Leica AF6000 live cell imager. Files can be saved in the proprietary Leica .LIF and .LEI formats or can be exported as TIFF or JPG files suitable for analysis with 3rd party image analysis software such as ImagePro or ImageJ.

Leica AF Lite

is a version of the LAF software with limited functionality but is freely down loadable from the vendor website. It primary use is to view files that were saved in the proprietary .lif and .lei formats

Image J

is a popular Java-based free-ware image analysis package developed at the NIH. Here's the Wikipedia summary of its history and applications: ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. 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. ImageJ's plugin architecture and built in development environment has made it a popular platform for teaching image processing. ImageJ can be run as an online applet, a downloadable application, or on any computer with a Java 5 or later virtual machine. Downloadable distributions are available for Microsoft Windows, Mac OS, Mac OS X, Linux, and the Sharp Zaurus PDA. The source code for ImageJ is freely available.

ImageJ can display, edit, analyze, process, save, and print 8-bit color and grayscale, 16-bit integer and 32-bit floating point images. It can read many image formats including TIFF, PNG, GIF, JPEG, BMP, DICOM, FITS, as well as raw formats. ImageJ supports image stacks, a series of images that share a single window, and it is multithreaded, so time-consuming operations can be performed in parallel on multi-CPU hardware. ImageJ can calculate area and pixel value statistics of user-defined selections and intensity thresholded objects. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as logical and arithmetical operations between images, contrast manipulation, convolution, Fourier analysis, sharpening, smoothing, edge detection and median filtering. It does geometric transformations such as scaling, rotation and flips. The program supports any number of images simultaneously, limited only by available memory.