Image Analysis Software


HALO (Indica Labs, Albuquerque, NM) software is a high performance, user friendly image analysis software. It can be used with confocal, wide field fluorescence, and bright field images. The HALO workstation is equipped with the following image analysis modules:

  • Area Quantification
    • Measure positive area, optical density, and stain co-localization for up to five stains in bright field images.
  • Area Quantification FL
    • Measure positive area, dye intensity, and dye co-localization of an unlimited number of fluorescent dyes. 
  • FISH Break-Apart/Fusion
    • Measure gene rearrangements detected using break apart/fusion probes.
  • FISH
    • Measure the number, intensity, and co-expression of an unlimited number of RNA/DNA probes on a per cell basis. Ideal for RNAScope analysis.
    • Measure the number, intensity, and co-expression of an unlimited number of RNA/DNA probes and IF protein bioamrkers on a per cell basis. Ideal for RNAScope analysis.
  • Highplex FL
    • Measure an unlimited number of fluorescent dyes in cell or tissue samples.
    • Measure IHC positivity, spot number, optical density, and co-expression of one or two bright field RNA or DNA probes.

NIS Elements

NIS Elements (Nikon Instruments Inc, Melville, NY) is an imaging and analysis software. Elements runs the Nikon A1R confocal microscope and N-Storm super resolution microscopes. In addition to the instrument computers, full versions of the software are available on the HALO and Metamorph workstations computers. It includes quantitation tools in the General Analysis suite, 2D and 3D tracking and measurement, and real time analysis of live cell dynamics. It can also be used to produce 2D projection images for 3D data and deconvolve both 2D and 3D images.

NIS - Elements Viewer User's Guide in a download format (738KB) This is the link to the free Nikon Elements Viewer software and user guide.



The MetaMorph software is on a dedicated computer using a 20 inch flat screen monitor with associated color printer. MetaMorph Offline software (Universal Imaging Corporation, a subsidiary of Molecular Devices) is a high end software package used extensively for image analysis, including colocalization, measurements of areas and distances and object counting and cell tracking with interactive user created regions of interest or automated analysis using an intensity threshold. All measurements are logged onto an Excel spreadsheet for subsequent analysis of data.

  • Colocalization
  • Object counting
  • Distance measurement
  • Area measurement
  • Cell tracking
  • 3D reconstruction

PerkinElmer Volocity 3D Rendering Software

Volocity (PerkinElmer, Waltham, MA) is a high-performance 3D imaging software package providing visualization, exploration andanalysis capabilities of multi-channel 3D volumes over time. The software can be used for 2D, 3D, and 4D imaging, and will accept image sequences from both confocal and wide-field microscopes. The Volocity Visualization module provides an extensive array of visualization and publication features. The Volocity 3D view enables the user to interactively explore a 3D rendered object. The viewing point can be placed either inside or outside of the 3D object, and changes of structures over time monitored. Animated movie volumes can be created with the Movie Sequencer module. The Volocity Classification module will identify, measure and track biological structures in 2D, 3D, and 4D. Co-localization analysis can also be performed for two fluorophores in 3D.


MBF StereoInvestigator Software

StereoInvestigator (MBF Bioscience, Williston, VT) image analysis software is designed to count cells, quantify lengths, area, and volumes in biological samples while employing stereological principles. With 13 stereological probes, it will efficiently allow you to obtain precise and unbiased estimates of cell number (Optical Fractionator probe), volume fractions (Cavalieri Estimator probe), or spatial distribution (Nearest Neighbor probe) of tissue components. Results can be exported directly into Microsoft Excel.

Papers published from the MIC:


  • Taatjes D.J.; Ghule P.N., B. N. A., Lee K., DeLance N.M., Evans M.F., Weaver D.L., Deakin N., Carr F.E., Sprague B.L., Stein G.S., Stein J.L. (2022). "The Shared Core Resource as a Partner in Innovative Scientific Research: Illustration from an Academic Microscopy Imaging Center." Journal of Biomedical Techniques 33(1).



  • Habibovic, A., et al. (2016). "DUOX1 mediates persistent epithelial EGFR activation, mucous cell metaplasia, and airway remodeling during allergic asthma." JCI Insight 1(18): e88811.
  • Mirando, A. C., et al. (2017). "Assessing the effects of threonyl-tRNA synthetase on angiogenesis-related responses." Methods 113: 132-138.
  • Thompson, J. K., et al. (2017). "Asbestos-Induced Mesothelial to Fibroblastic Transition Is Modulated by the Inflammasome." Am J Pathol 187(3): 665-678.
  • van der Velden, J. L., et al. (2018). "TGF-beta1-induced deposition of provisional extracellular matrix by tracheal basal cells promotes epithelial-to-mesenchymal transition in a c-Jun NH2-terminal kinase-1-dependent manner." Am J Physiol Lung Cell Mol Physiol 314(6): L984-L997


  • Gillis, N. E., et al. (2018). "Thyroid Hormone Receptor beta Suppression of RUNX2 Is Mediated by Brahma-Related Gene 1-Dependent Chromatin Remodeling." Endocrinology 159(6): 2484-2494.
  • Smith, K. P., et al. (2016). "Inner-membrane protein MorC is involved in fimbriae production and biofilm formation in Aggregatibacter actinomycetemcomitans." Microbiology 162(3): 513-525.
  • Tracy, K. M., et al. (2018). "Mitotically-Associated lncRNA (MANCR) Affects Genomic Stability and Cell Division in Aggressive Breast Cancer." Mol Cancer Res 16(4): 587-598.

Additional publications located here.

HALO Example Markup Image Elements_GA3 imageanalysis_152x267 Volocity- biofilm reconstruction R17-238_007 with markers