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Go from assay to insights quickly and reliably with ImageXpress imaging systems and IN Carta software


IN Carta® Image Analysis Software solves complex image analysis problems utilizing advanced Artificial Intelligence (AI) transforming images into data. Easy-to-use workflows help you get answers faster from 2D, 3D, and time-lapse experiments. With the integration of MetaXpress® Custom Module Editor application, you can define your own image analysis protocols allowing you to quickly visualize, review, and interact with the analysis results. Let IN Carta software do the heavy lifting so you can focus on your research.

  • Powerful


    Guided workflows and scalable batch processing increase productivity and reduce time to answer. Experiments can be set up quickly and computational resources can run analysis of multiple wells in parallel efficiently.

  • Insightful


    Machine learning helps you leverage more information and increase accuracy in the analysis of high-content screening data to enable new discoveries with confidence.

  • Intuitive


    Modern user experience and cutting-edge technology minimizes the software learning curve and removes barriers to productivity.

In Carta Image Analysis Software

In Carta Image Analysis Software


  • Machine learning

    Machine learning

    Improve image analysis workflow with SINAP and phenoglyphs modules for AI-driven solutions. SINAP uses deep learning for robust image segmentation. Phenoglyphs uses machine learning-based classification to reveal insights from complex datasets.

  • 3D Analysis

    3D Analysis

    Segment and quantify biological structures in 3D. IN Carta VoluMetrics module provides algorithms that operate on voxels when segmenting objects and extracting informative measures.

  • Customization


    Browse and review images from experiments, create image analysis protocols, process data, and visualize analysis results.

  • Worklists


    Browse to a parent directory and populate your worklist with image datasets of interest.

  • Batch analysis

    Batch analysis

    Analyze multiple experiments in batch analysis mode with one or more analysis protocols.

  • Monitoring

    Monitor the status of all submitted batch analysis tasks and oversee their progression in real time.


SINAP is a module that uses deep learning algorithms to improve accuracy and reliability of high-content screening assays at the first step in the analysis pipeline—segmentation. It provides better object detection than traditional image analysis methods. Quantitative information extracted at this step is more accurate so errors are notcontent-section propagated down the analysis pipeline.

With SINAP, Segmentation Is Not A Problem!

  • Accurate - deep learning can maintain accuracy across difficult to segment samples including highly confluent cells and low signal-to-noise samples
  • Reliable - SINAP models can account for high phenotypic variability
  • Flexible - a single workflow can deal with a variety of applications and imaging modalities, including challenging fluorescent and transmitted light assays
  • Accessible - trained model learns to segment from users drawing on the image rather than asking the user to develop an image processing pipeline and optimize multiple parameters
Composite of segmentation masks for nuclei (blue), endoplasmic reticulum (green), mitochondria (fuchsia)

IN Carta Phenoglyphs

IN Carta® Phenoglyphs™ Software Module uses advanced machine learning to classify segmented objects. Using many hundreds of cellular features that can be analyzed simultaneously, a comprehensive phenotypic profile is created and can be applied throughout an entire screening workflow. This multivariate approach to classification provides accurate characterization of object populations allowing users to resolve subtle phenotypic changes induced by drug treatment or genetic modification. It can be utilized across many biological targets including organoids, cells, spheroids, and more.

IN Carta Phenoglyphs
  • Robust – the novel unsupervised step in the workflow quickly builds a large unbiased training set that captures the variance in a class and produces models that are less subject to overfitting and misclassification
  • Comprehensive – a data driven approach that starts with an unsupervised clustering to find patterns in the data and highlight subpopulations without prior knowledge of what phenotypes may exist
  • Optimized workflow – machine learning automatically chooses the optimal set of descriptive features to form a complex set of rules to stratify classes. Classification is achieved by simply confirming or correcting the algorithm’s predictions until it learns the right behavior.

IN Carta VoluMetrics

3D biological models that more accurately mimic in vivo organs and tissues show great potential as tools to improve the understanding of disease and probe for potential therapies. IN Carta VoluMetrics is a 3D image analysis module that extends IN Carta software’s functionality with the ability to segment and quantify biological structures in 3D.

IN Carta VoluMetrics provides algorithms that operate on voxels when segmenting objects and extracting informative measures. This provides a better representation of the sample morphology and intensity distributions compared to individual Z-plane analysis where the relationship between objects in adjacent Z-planes is a rough approximation.

IN Carta VoluMetrics

IN Carta VoluMetrics

Random color segmentation masks that assess segmentation quality of touching objects in densely packed spheroids

ImageXpress® Confocal High-Content Imaging System

Powerful multi-laser light sources, a deep tissue penetrating confocal disk module, water immersion objectives and modern machine learning analysis software

  • Ideal for highly complex cell-based and 3D assays
  • Seven-channel high-intensity lasers generating brighter images with higher signal-to-background ratio
  • Spinning confocal disk technology for deeper tissue penetration, resulting in sharper images with improved resolution
  • Water immersion objectives offering up to quadruple the signal at lower exposure times for greater sensitivity and image clarity
  • View product

StratoMineR Advanced Cloud-Based Analytics

Generate clear, deep data from complex datasets

Powerful and intuitive workflows allow users to port high-content imaging data directly into StratoMineR where it is used to generate rich, interactive visualizations using advanced data mining methods. When used with IN Carta Image Analysis Software, it provides robust, quantitative results from complex biological images and datasets utilizing advanced AI technology. Use all of your high-content data to discover, characterize, and analyze Phenotypes.

Latest Resources


  • Live Cell Imaging

    Live Cell Imaging

    Live cell imaging is the study of cellular structure and function in living cells via microscopy. It enables the visualization and quantitation of dynamic cellular processes in real time. Live cell imaging encompasses a broad range of topics and biological applications—whether it is performing long-term kinetic assays or fluorescently labeling live cells.

    Learn More  

Resources of IN Carta Image Analysis Software

Videos & Webinars
Emerging Organoid Models

Emerging Organoid Models: Translating Basic Research to Drug Development and Regenerative Medicine

Automating culture and high-content imaging

Automating culture and high-content imaging of 3D organoids for in vitro assessment of compound effects

Deep Learning-Based Image Analysis

Deep Learning-Based Image Analysis for Label-Free Live Monitoring of iPSC and 3D Organoid Cultures

Monitoring organoid development in iPSC-derived 3D cerebral

Monitoring organoid development in iPSC-derived 3D cerebral organoids

Automated Culture and High-Content Imaging of 3D Lung

ISSCR 2021 Innovation Showcase: Automated Culture and High-Content Imaging of 3D Lung and Cardiac

Explore our high-content imaging portfolio

High-content imaging and analysis solutions, ranging from automated digital microscopy to high-throughput confocal imaging systems with water immersion objectives and proprietary spinning disk technology.