Incucyte® Base Analysis Software

The Incucyte® Base Analysis Software simplifies the complex yet provides a powerful workflow that supports your entire research team.

A guided interface and purpose-built tools make the process of acquiring, viewing, analyzing and sharing images of living cells easier than ever before using the Classic or new AI-driven Analysis.


Stress-free Image Acquisition

  • Guided interface enables even first-time users to set up long-term, live-cell experiments
  • Flexible scheduling tool allows multiple users to run multiple applications in parallel

Insight-generating Visualization

  • Incucyte® VesselView displays a birds-eye view of the entire vessel to give you a snapshot of your experiment, plus tools to quickly navigate through images and time
  • Quickly assess trends and outliers, and validate with metric overlays

Powerful, Purpose-built AI-driven Analysis

  • Guided interface makes processing thousands of wells of data easier, driven by AI or Classic segmentation
  • Graphing tools designed by biologists enable publication-ready graphs without the need for third-party software

Incucyte® Base Software Workflow

Incucyte® AI Confluence Analysis Workflow

AI-driven Confluence Analysis provides a simple workflow for highly accurate segmentation of cells in phase contrast images, adapting to a wide range of cell types and morphologies with minimal user input. AI Confluence Analysis is available with Incucyte® Software v2022A. 

Incucyte® Classic Confluence Analysis Workflow

The Classic Confluence Analysis enables you to tailor phase segmentation parameters to individual cell types and experimental conditions to accurately distinguish between background and positive fluorescent objects across a wide range of intensities, and depending on the optical module, allows for the quantification of green, orange, red, and/or NIR fluorescent objects within each image.

Incucyte® Base Software  Overview


Incucyte® Acquisition interface guides users through experimental set up using your choice of microplates, flasks and dishes. Simply select parameters and hit “Start” for fool-proof, continuous live-cell image acquisition.


Incucyte® VesselView enables users to navigate and explore thousands of timelapse images with unprecedented efficiency. By viewing images of all locations in your experiment at once, you can quickly assess treatment effects or identify outliers. You can also overlay metrics for rapid assessment and verification of image processing parameters. Then, generate presentation-ready images and movies with just a few clicks.

Easily view images of all locations in an experiment at once to scan for trends and outliers, then zoom in on wells of interest.


Incucyte® Analysis interface enables even first-time users to convert images into insights. By providing purpose-built tools to answer your scientific questions, image processing and analysis is uncomplicated yet extremely powerful. Create analysis definitions once, then reapply to subsequent experiments to generate real-time metrics that enable decision-making. Easily view all trends in an experiment at once with Incucyte® Microplate Graphs, and create customized response curves that are ready for publication and presentation

Guided analysis interface enables even first-time users to convert images into insights using powerful AI-driven or classic segmentation for confluence measurements.

Graphing tools enable review of trends and rapid generation of publication- and presentation-ready graphs.

Ordering Information

Incucyte® Base Software

Software Module


Cat. No.

Incucyte® Base Software

User-friendly software suite for image acquisition, viewing, and analysis

Included with Incucyte® Live-Cell Analysis System

Add-on Software Modules

Software Module


Cat. No.

Incucyte® Advanced Label-Free Classification Analysis Software ModulePerform counts and track changes in adherent cell morphology via label-free image segmentation and multivariate analysis of cell shape. Classifier is trained using control wells. Module an adds-on and requires Incucyte® Cell-by-Cell Analysis Software Module.


Incucyte® Cell-by-Cell Analysis 
Software Module

Perform label-free cell counts and subsequent cell-by-cell classification based on shape, size or fluorescence intensity to quantify dynamics changes in cell subsets within heterogenous living cell cultures.


Incucyte® Organoid Analysis 
Software Module

Characterize the differentiation and maturation of organoid cultures in 24- or 48- well plates and assess treatment effects on organoid growth in 96-well microplates.


Incucyte® Spheroid Analysis 
Software Module

Analyze growth, viability or invasion of single spheroids in round- bottom multi-well format or measure multiple spheroid in flat bottom plates to detect changes of growth or viability.


Incucyte® Neuronal Activity Analysis Software Module

Purpose-built acquisition and analysis for detection of Ca2+ oscillation in 96-well plates.


Incucyte® Neurotrack Analysis Software Module

Enables label-free or fluorescence analysis of neurite outgrowth, maturation or disruption in each well in 96- or 384-well plates.


Incucyte® Chemotaxis Analysis Software Module

Track and quantify label-free and fluorescence labeled chemotaxis cell migration and invasion in microplate format.


Incucyte® Scratch Wound Analysis Software Module

Analyze 96-well Incucyte® Scratch Wound Assay images to quantify cell migration and invasion with or without labels.


Incucyte® Angiogenesis Analysis Software Module

Assess complex network development and disruption qualitatively to study therapeutic interventions of vascular formation.


Incucyte® Base Software Resources

Incucyte - Empower Live-Cell Analysis Inside Your Incubator

Incucyte® Instrument Brochure

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Incucyte® RCS Brochure

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Updated Basic Analyzer Guidelines 

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live cell analysis

Incucyte® Live Cell Analysis System

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

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Incucyte® Incustore

Ideal if you use your Incucyte intensively as it keeps data on-line and at your fingertips for longer. The RAID 6 configuration of 8 x 6TB hard disks...

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