IncuCyte® Software

Enable powerful long-term phenotypic cellular analysis in real time

The most up-to-date software for the IncuCyte® ZOOM Live-Cell Analysis system. Version 2016B provides enhanced user-friendly control of all aspects of imaging and analysis including powerful and intuitive image processing tools.

2016B Release

2016B Key Enhancements

Enhanced Support for Single Spheroid Applications

  • New autofocus algorithm specifically designed for single spheroids cultured in round bottom ULA plates
  • Support for new round bottom ULA plates

See our complete list of compatible vessels in 2016B

2016A Release

2016A Key Enhancements

Coincident Object Analysis (COA)

Automatically quantify red and green fluorescence overlap. Selectively analyze co-labelled objects and measure changes in fluorescence coincidence over time.

The IncuCyte® Coincident Object Analysis tool enables calculation of the total number, and area, of overlapping objects. Example applications include:

  • Selectively analyze labelled sub populations — differentiate between red, green and co-labelled objects
  • Monitor co-expression of genes or fluorescent biomarkers — measure changes in co-expression over time
  • Demonstrate cellular localization of proteins — quantify internalization

Coincident Object Analysis (COA) Quick Guide

  1. Create a suitable image mask for the green fluorescent objects – filter out objects that you do not wish to include in the Coincident Object Analysis.
  2. Create a suitable image mask for the red fluorescent objects – filter out objects that you do not wish to include in the Coincident Object Analysis.
  3. Navigate to the Overlap (Analyse) command tab. Check the ‘Analyse’ box.
  4. The software will create a 3rd mask (Overlap) based on the overlap of the red and green image masks. This overlap mask can also be filtered for size (to eliminate small or large objects) if required.
  5. Run the analysis job; the mask and overlap metrics can be visualised and plotted in the IncuCyte software in the same ways as other channel metrics. For fluorescent masking guidelines refer to the technical note (IncuCyte® ZOOM Fluorescent Processing overview).

Download the IncuCyte® Coincident Object Analysis User Guide

Worked example: BHK-21 cells were simultaneously cotransfected with two foot-and-mouth disease virus (FMDV) replicons containing either a GFP (green) or mCherry (red) reporter cassette in place of the structural proteins (as described previously, Herod et al, JGV, 96:3507-6518). Coincident object analysis was used to quantify the proportion (area metric) of cells expressing one (green or red) or both (yellow) of the replicons over time. This approach can be used to study the interactions of cells containing two replicons. Data courtesy of Dr. Morgan Herod (University of Leeds).

Coincident Object Analysis (COA) Frequently Asked Questions

Q: What metrics does COA return?

The coincident objects are quantified by count (number of objects) and area (µm2). As with other object metrics, count data can be displayed as units per image, per well or per mm2. Area metrics can be displayed as units per image or units per well.

Q: I cannot see any intensity metrics in the Overlap channel. Why is that?

A: The Overlap mask does not take into account the intensities of the green or red fluorescent channels, but simply quantifies the overlay of the masked areas (area or count). The individual red or green fluorescent masks can be adjusted for object intensity thresholds – this will change the masked area in that channel as well as the related COA mask.

Q: Can I export the COA metrics into other programs, e.g. Microsoft Excel?

A: Yes, the COA (Overlap) metrics can be exported using the same method as for all other metrics.

Q: Can I use COA to calculate the percentage of green objects that are red, or vice-versa?

A: Yes, the overlap metrics can be normalised to the individual fluorescent channels to calculate a % value. This feature is not available within the IncuCyte software - the data must first be exported to an analysis package such as Microsoft Excel to make this calculation.

Q: Can I reference either of the fluorescent channels to the phase channel, and measure COA for phase contrast/green or phase contrast/red?

A: Not currently. Whilst the phase contrast channel is not available for the overlay analysis, the phase metrics may prove useful for normalisation (cf Q4 above).

Q: Is there anything I need to be aware of when comparing the time-courses of green and red fluorescent objects?

A: The COA metrics allow quantification of the relationship between the time-courses of the green and red fluorescent channels (e.g. when did red objects appear and coincide with green objects). However, the user should be aware that differences in the masks of the individual channels can create apparent differences in the time-courses – the impact of this is amplified when two masks are compared to return the COA. Care should be taken (1) in ensuring that the fluorescent masks faithfully describe the fluorescent objects, and (2) when interpreting small differences in time-courses across fluorescence channels

2015A Release

2015A Key Enhancements

Added capability of 384-well whole-well imaging

  • Image the entire surface of every well using High-Definition phase contrast optics
  • Perform dilution cloning studies in high throughput format with automated imaging and colony detection
  • High-Definition phase contrast clarity enables clear detection of single cells even at well edges enabling easy verification of monoclonality

Enhanced NeuroTrack® fluorescence tools

  • Improved sensitivity ensures fluorescently labeled neurons are accurately detected whether dim or bright
  • Enables the use of a wider range of neuronal labels with varying fluorescence intensities

New fluorescence analysis tools for co-culture scratch wound assays

  • Monitor and measure migration of fluorescently labeled cells in co-culture models (e.g. test the effect of stromal cells on cancer cell migration)
  • Correlate migration potential with gene expression or activation/inhibition of signaling pathways

Improved scheduling flexibility using the new Restore feature

  • The “Restore” feature allows users to use individual tray positions for more than one experiment at a time
  • Interrupt experiments and resume at a later date using any tray position in the confidence that your data will be automatically paired with previous scans
  • Conduct an experiment over many days without tying up the instrument

Compare versions

IncuCyte® ZOOM Software Version Feature Comparison

Features and Functionalities Version
2013B 2014A 2015A 2016A 2016B
Data Storage
Data Archiving
IncuStore™ Expansion Data Storage Compatibility
Whole Well Imaging
Points of Interest (POIs) - Digital Monitoring Tools
Automated vessel marking - IncuCyte ZOOM® Marking Tool
35mm Dishes, 6-, 12-, 24-, 96-Well Enabled
384-Well Enabled
General Features
New Movie Formats (MPEG-4, AVI uncompressed)
Improved Scheduling Flexibility
Fluorescence Analysis Tools for Co-culture Scratch Wound Assays
Enhanced IncuCyte® NeuroTrack  Fluorescence Tools
Enhanced autofocus and additional plate support for single spheroid applications in round bottom ULA plates    
Data Processing
Background Fluorescence Subtraction
Fluorescent NeuroTrack™ Analysis
Import/Export Image Processing Definitions
Coincident Object Analysis
IncuCyte ZOOM® Rack System
Space Saving Rack - Holds 2 instruments and 2 IncuStore™ Units
Uninterruptable Power Supply
'In The Lab' Access to User Interface
Enabled Applications
Cell Culture QC
Clonal Dilution
Immune Cell Killing
Immune Cell Proliferation & Clustering
Neurite Dynamics - Label-free*
Neuronal Co-Culture - Fluorescence*
Proliferation - Cell Count
Proliferation - Confluence
Reporter Gene
Scratch Wound Migration*
Stem Cell Monitoring & Reprogramming
Transfection Efficiency

* additional software module required

Software update

How to Update Your Software

  1. If under warranty, update for free - If your IncuCyte® ZOOM instrument is within the warranty, the update is free by clicking on the button below, or
  2. Purchase an extended warranty - If your IncuCyte® ZOOM instrument is out of warranty, you need to purchase the IncuCyte® Extended Warranty, which includes the software update.

Learn more about IncuCyte ZOOM® Live-Cell Analysis System Request Software update


Gain insights into biological processes of cells in real time via non-perturbing quantitative analysis

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