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IN Carta Image Analysis Software

Provides robust, quantitative results from complex biological images and datasets
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.
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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.
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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.
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Intuitive
Modern user experience and cutting-edge technology minimizes the software learning curve and removes barriers to productivity.
In Carta Image Analysis Software
Features
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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.
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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.
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Customization
Browse and review images from experiments, create image analysis protocols, process data, and visualize analysis results.
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Worklists
Browse to a parent directory and populate your worklist with image datasets of interest.
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Batch analysis
Analyze multiple experiments in batch analysis mode with one or more analysis protocols.
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Monitoring
Monitor the status of all submitted batch analysis tasks and oversee their progression in real time.
IN Carta SINAP
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.

- 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.
Random color segmentation masks that assess segmentation quality of touching objects in densely packed spheroids
ImageXpress® Confocal HT.ai 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
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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.
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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.
Resources of IN Carta Image Analysis Software
Application Note
Automation and high content imaging of 3D triple-negative breast cancer patient-derived tumoroids assay for compound screening
Automation and high content imaging of 3D triple-negative breast cancer patient-derived tumoroids assay for compound screening
Triple negative breast cancer is a clinically aggressive tumor subtype, with high rates of metastasis, recurrence, and drug resistance.
Publications
A Picture Paints a Thousand… New Therapies?
A Picture Paints a Thousand… New Therapies?
Cell painting is a high-content profiling technology that uses up to six fluorescent dyes to visualize specific cellular components at the single-cell level. The assay essentially “p…
Brochure
StratoMineR
StratoMineR
Core Life Analytics’ StratoMineR™ software helps biologists analyze the complex data derived from high-content image analysis. A powerful, intuitive workflow allows users to port dat…
Application Note
Increase Cell Painting assay throughput using an automated workstation
Increase Cell Painting assay throughput using an automated workstation
Cell painting has become a popular screening method within the drug discovery community. This phenotypic screening platform leverages advances in high-content microscopy, high-…
Publications
Benefits of Real-Time Live-Cell Imaging
Benefits of Real-Time Live-Cell Imaging
Three-dimensional (3D) cell-based assays replace a host of tissue, cell, and animal test models but have a reputation for lacking time resolution. For e…
Scientific Poster
Phenotypic profiling based on the Cell Painting assay
Phenotypic profiling based on the Cell Painting assay
Multiparametric high-content screening approaches, such as the Cell Painting assay, are increasingly being used in many applications ranging from drug discovery programs to functiona…
Scientific Poster
Intestinal organoids for automated screening assays. High content imaging and analysis of organoid morphology
Intestinal organoids for automated screening assays. High content imaging and analysis of organoid morphology
3D cell models representing various tissues were successfully used for studying complex biological effects, tissue architecture, and functionality. However, complexity of 3D models r…
Application Note
Label-free cell segmentation with IN Carta SINAP application module
Label-free cell segmentation with IN Carta SINAP application module
Label-free cell analysis provides a better alternative to using fluorescent dyes as it enables scientists to image live cells under near-native conditions – examining biological…
Blog
Engineering Next-gen Organoids with Automated Lab Workflows at #SLAS2022
Engineering Next-gen Organoids with Automated Lab Workflows at #SLAS2022
SLAS2022, the Society for Lab Automation and Screening conference offered another exciting year for learning about innovative laboratory technologies. Whether you attended in-person…
Application Note
Improving the robustness of Cell Painting with a near-infrared label and advanced image and data analytics
Improving the robustness of Cell Painting with a near-infrared label and advanced image and data analytics
Image-based phenotypic profiling approaches such as the widely used Cell Painting assay use high-content imaging along with multiparametric readouts to study biological, genetic, and…
Scientific Poster
Automation of 3D organoid culture workflow with deep-learning based image analysis
Automation of 3D organoid culture workflow with deep-learning based image analysis
3D cell culture as a model system is increasingly popular because it recapitulates the in vivo microenvironment better than 2D cell cultures. Organoids have the capacity for stable d…
Scientific Poster
Automation and high content imaging of 3D triple-negative breast cancer patient-derived
Automation and high content imaging of 3D triple-negative breast cancer patient-derived
Triple negative breast cancer is a clinically aggressive tumor subtype, with high rates of metastasis, recurrence, and drug resistance. Currently there are no clinically approved sma…
Scientific Poster
Improving the robustness of Cell Painting with a near-infrared label and advanced image and data analytics
Improving the robustness of Cell Painting with a near-infrared label and advanced image and data analytics
Image-based phenotypic profiling approaches, such as the widely-used Cell Painting assay, use high-content imaging along with multiparametric readouts to study biological, genetic, a…
Application Note
Deep Learning-based Image Analysis for Label-free Live Monitoring of iPSC and 3D Organoid Cultures
Deep Learning-based Image Analysis for Label-free Live Monitoring of iPSC and 3D Organoid Cultures
Complex 3D biological models such as organoids and patient-derived spheroids are gaining popularity in many biomedical research areas because they more closely recapitulate the in vivo…
Blog
Innovation at Molecular Devices: Updates in Automated, High-Content Imaging
Innovation at Molecular Devices: Updates in Automated, High-Content Imaging
From customer feedback to workflow improvements The path to understanding complex biological processes and diseases is paved with a lot of challenges. As the desired level of…
Blog
Stem cell science insights and breakthroughs presented at #ISSCR2021
Stem cell science insights and breakthroughs presented at #ISSCR2021
If you didn't get a chance to visit us at our poster sessions during ISSCR 2021, don’t fret. We've gathered all our sessions right here for you. The ISSCR Annual Meeting brought…
Application Note
Organoids for disease modeling and in vitro drug screening
Organoids for disease modeling and in vitro drug screening
3D cell models representing various tissues were successfully used for studying complex biological effects, tissue architecture, and functionality. However, the complexity of 3D models…
Publications
Project Profile: Organoid Innovation Center
Project Profile: Organoid Innovation Center
Lab Manager speaks to Dan O’Connor, vice president, drug discovery, Molecular Devices, about the company’s Organoid Innovation Center in San Jose, CA. The center is 180 sq. ft., with…
Publications
Organs-on-Chips: Expand the Boundaries of In Vitro Testing
Organs-on-Chips: Expand the Boundaries of In Vitro Testing
Humans began culturing animal cells and tissues as early as the late 19th century, when Wilhelm Roux first showed that chick embryos could be cultured in saline solution for a few da…
Brochure
IN Carta Image Analysis Software
IN Carta Image Analysis Software
IN Carta™ Image Analysis Software solves complex image analysis problems utilizing advanced Artificial Intelligence (AI) turning images into data. Easy-to-use workflows help you get…
Blog
Tips for running a successful live cell imaging experiment
Tips for running a successful live cell imaging experiment
There have been significant advancements in microscopy and camera technology, as well as advancements in technologies for labeling molecules of interest over the past decade. These…
Publications
Shaping the Future of Organoid Research
Shaping the Future of Organoid Research
Molecular Devices, a provider of innovative life science technology, recently unveiled a brand new, first-of-its-kind Organoid Innovation Center. Situated at the company’s global hea…
Blog
Overcome the challenges of high-content cell analysis through AI/machine learning
Overcome the challenges of high-content cell analysis through AI/machine learning
Artificial intelligence (AI) is finding its way into many aspects of modern life, from autonomous vehicles to voice-powered personal assistants, and even the creation of art. But it…
Blog
How Cell Painting is making its mark on drug discovery
How Cell Painting is making its mark on drug discovery
Have you ever heard the old adage, “A picture is worth a thousand words?” When it comes to Cell Painting, this saying is especially true. Cell Painting is a high-content,…
Publications
Danaher’s SCIEX and Molecular Devices Businesses Debut New Products
Danaher’s SCIEX and Molecular Devices Businesses Debut New Products
It has been a busy beginning of the year for Danaher’s Life Sciences segment. In January, the business reported 2020 revenues of $10.6 billion, represen…
Blog
Life sciences technology predictions for 2021
Life sciences technology predictions for 2021
For over 30 years, Molecular Devices has been at the forefront of technological advances which have contributed to significant scientific breakthroughs. To kick off the new year, we…
Publications
Rising growth of the global high‑content screening software and services market
Rising growth of the global high‑content screening software and services market
Developments in informatics solutions and high-content imaging instruments, increased focus on cell-based research, and rising government support of research and development for drug…
Brochure
Innovative Solutions for Drug Discovery and Life Sciences Research
Innovative Solutions for Drug Discovery and Life Sciences Research
Molecular Devices is a leading provider of high-performance bioanalytical measurement solutions for life science research, pharmaceutical development, and biotherapeutic discovery. O…


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

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

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

Monitoring organoid development in iPSC-derived 3D cerebral organoids

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.
Advanced Cloud-Based Analytics with StratoMineR
Increase efficiency and throughput with cloud-based advanced analytics

IN Carta Image Analysis Software
Provides robust, quantitative results from complex biological images and datasets

Cellular Imaging Systems
Transform your incredible images into captivating results
How can we help advance your next big discovery?
Our highly-qualified teams are on the frontlines with our customers, conducting remote or on-site product demonstrations, webinars, and more to help you solve your tough research challenges. How can we help you today?
I’d like to…
How can we help advance your next big discovery?
Our highly-qualified teams are on the frontlines with our customers, conducting remote or on-site product demonstrations, webinars, and more to help you solve your tough research challenges. How can we help you today?
I’d like to…