Powering Discovery with AI
Quantitative and intuitive image analysis for pathology
Image Analysis Simplified
With unmatched ease-of-use and scalability, powerful analytic capabilities, and the fastest processing speeds available for digital pathology, research, pharma and healthcare organizations worldwide are using HALO® for high-throughput, quantitative tissue analysis.
Intuitive Platform for Analysts at All Levels
An image analyst can be up and running with basic analysis functions in just a couple of hours with the user-friendly HALO platform – even with no prior image analysis experience!
HALO modules simplify the analysis workflow so there is no need to ‘build’ algorithms from scratch. Our purpose-built modules make HALO easy-to-use and understand which means you can spend less time learning software and more time analyzing data.
Extensive Analytics, Reliable Results
HALO reports morphological and multiplexed expression data on a cell-by-cell basis across entire tissue sections while maintaining an interactive link between cell data and image. Sort and filter cell data to mine millions of cells while also visually assessing cell populations in the context of tissue architecture, leverage interactive markups to understand colocalization and explore combined phenotypes, and define custom analysis outputs.
Leverage Integrated AI Tools
Use pre-trained deep-learning networks for optimized nuclear and membrane segmentation directly in the HALO platform with cell analysis modules in brightfield or fluorescence, including the Multiplex IHC and Highplex FL modules.
Want to train your own AI? Learn more about HALO AI.
Rapid Analysis and Efficient Workflows on a Scalable Platform
Increase your productivity with multi-core processing and batch analysis or with workflow tools for efficient tissue microarray and serial stain analysis.
1. Choose Modules
Options include analysis and workflow modules.
2. Choose License
Single seat, multiple seat & enterprise license options available.
3. Choose Term
License HALO on an annual or permanent basis.
4. Choose Deployment
Manage your own local or cloud deployment, or work with Cloud Services.
The modular design and flexible licensing of HALO allow it to be adapted to any requirement. Start with a few modules and add more as your needs change. Use HALO on a single workstation, on a server-based license or deploy enterprise wide. Choose either a permanent license or renew annually and choose the deployment option that works best for your team and local IT.
Highly Interoperable Ecosystem
HALO has a variety of data export and import tools so that you can work with your data outside of the HALO platform and then bring it back in.
HALO also seamlessly integrates with our deep learning toolbox HALO AI, our study-based image management system, HALO Link, and our case-based image management system, HALO AP®.
Want to connect to another image management system? Custom integrations are available using a powerful and open GraphQL API. Reach out to info@indicalab.com to learn more.
Contribute to the Growing List of High Impact HALO Publications
HALO image analysis appears in over 1,600 peer-reviewed publications and every year the number of publications continues to grow!
Our customers publish across a wide range of disciplines and research areas, with oncology and immuno-oncology leading the publication count, shortly followed by neuroscience, metabolism, immunology, and infectious disease.
Curious to learn more? Check out the Publications tab in the HALO Knowledge Center.
HALO® Peer-Reviewed Publications
Top Notch Training and Support
We’ve worked hard to ensure HALO is the most intuitive image analysis platform in the industry, but we realize that you may still need extra support. We’ve got you covered!
Unlimited IT support, scientific support, training, and access to the Learning Portal are included with every license at no additional cost. With support staff in the US, UK, EU, China, and Japan, you are supported in any time zone.
The vast majority of our new customers heard about Indica Labs from an existing customer. The two primary reasons for referral – our user-friendly technology and excellent support. We know that you have a choice in image analysis providers, and we strive to make sure every customer is 100% satisfied.
Platform Compatibility
File Formats:
- Non-proprietary (JPG, TIF, OME.TIFF)
- Nikon (ND2)
- 3DHistech (MRXS)
- Akoya (QPTIFF, component TIFF)
- Olympus / Evident (VSI)
- Hamamatsu (NDPI, NDPIS)
- Aperio (SVS, AFI)
- Zeiss (CZI)
- Leica (SCN, LIF)
- Ventana (BIF)
- Philips (iSyntax, i2Syntax)
- KFBIO (KFB, KFBF)
- DICOM (DCM*)
*whole-slide images
HALO® is compatible with a broad spectrum of image and digital slide formats. Yours not on the list? Email us your requirements.
Powering Discovery with AI: Features of the HALO Image Analysis Platform
Optimize fluorescent image visualization using powerful view settings capabilities. Compare channel histograms of multiple images, track intensity values in the histogram per channel, leverage an autofit calculation, and apply settings in batch.
With pre-trained AI-based networks for nuclear and membrane segmentation available in both brightfield and fluorescence, optimizing your segmentation parameters has never been easier.
Identify cell types of interest with the streamlined phenotype editor feature. Assign channel combinations using an intuitive grid interface, visualize phenotypes using the real-time tuning feature, and export phenotype settings as .csv files.
Customize image analysis outputs and set up calculations prior to running analysis to create exactly the data you need.
Investigate results with interactive markup images where you can toggle on and off each cell population of interest.
Use saved analysis settings to queue up a batch analysis in just a few clicks. Continue to work in HALO while the automated analysis runs on the back end.
Acquire publication quality figures in just a few clicks with the figure maker feature. Quickly define the number of frames, select images of interest from across studies, then optimize reference frames, scale bars, labels, and more. Save figures to edit later or download at your desired image size and resolution.
Discover HALO® Modules
Explore our most popular HALO modules & add-ons. You can filter by category and use the arrows at the bottom of the list to view additional options.
Quantify expression of an unlimited number of biomarkers in any cellular compartment - membrane, nucleus or cytoplasm.
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Quantify expression of up to five brightfield stains in any cellular compartment - membrane, nucleus or cytoplasm.
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Acquire deeper insights into complex data sets using dimensional reduction and unsupervised clustering with interactive plotting.
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Plot cells and objects from one or more images and perform nearest neighbor analysis, proximity analysis, and tumor infiltration analysis.
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Use the HALO® FISH-IF module and reagents from Molecular Instruments or ACD, a Bio-techne brand, to simultaneously analyze an unlimited number of fluorescently-labeled DNA/RNA ISH probes and immunofluorescent protein biomarkers on a cell-by-cell basis.
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Simultaneously analyze up to three chromogenic and/or silver-labelled DNA or RNA ISH probes on a cell-by-cell basis, measuring spot numbers and area per cell and compartment, and calculated H-scores for each probe.
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Simultaneously analyze a nuclear stain and up to four IHC biomarkers or ISH probes on a cell-by-cell basis across brightfield images.
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Simultaneously analyze an unlimited number of fluorescent nucleic acid probes on a cell-by-cell basis, measuring spot numbers and area per cell and compartment, and calculated H-scores for each probe.
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Separate multiple tissue classes across a tissue using a learn-by-example approach. Can be used in conjunction with all other modules (fluorescent and brightfield) to select specific tissue classes for further analysis.
Learn MoreWhat Our Customers Have to Say
Read independent reviews on our HALO image analysis platform and learn how these customers are using Indica Labs’ solutions to streamline their workflows.
Deploy HALO® in a Fully Managed Cloud-Hosted Environment
Indica Labs offers optimized deployments of HALO software hosted in Amazon Web Services (AWS). We manage all aspects of implementation and ongoing maintenance to provide a highly performant, scalable, and secure HALO environment in the cloud.
You maintain full ownership over your AWS account while our AWS Certified Solutions Architects manage your infrastructure and HALO software environments.
Learn more about benefits of cloud-hosted environments in our recent blog post. Or reach out today to our Cloud Services team by using the form below, to learn whether a managed cloud deployment is right for you.
Knowledge Center
Learn more about HALO® image analysis by exploring the tabs below.
COMET™ and RNAscope™ Image Analysis Using HALO and HALO AI
Read this collaborative app note to learn how our Pharma Services team leveraged the HALO FISH-IF and Spatial Analysis modules and HALO AI for analysis of COMET™ and RNAscope™ images.
Spatial Analysis Application Note
In this application note, we describe two HALO analysis tools that are used to quantify the distribution of immune cells relative to tumor cells in the tumor microenvironment, Proximity Analysis and Tumor Infiltration Analysis.
Fusion of Spectrally Unmixed Image Tiles into Whole Slide TIFs using HALO Image Analysis
In this application note, we describe how HALO can convert spectrally unmixed image tiles into whole slide images for analysis of the tumor microenvironment.
RNAscope™ Image Analysis Using HALO and HALO AI
Using our ISH module for brightfield and our FISH module for fluorescence, we demonstrate how to quantify ISH signal from RNAscope® assays on a per cell or per unit area basis and output an overall expression score based on ACD Bio’s recommended scoring guidelines.
HiPlex RNAscope™ Application Note
Using our FISH module we demonstrate how to perform 12-plex RNAscope image analysis using ACD’s HiPlexv2 assay.
HALO Platforms for Life Sciences Brochure
Download our brochure to learn about our HALO, HALO AI, and HALO Link platforms, and how they can advance your digital pathology image analysis and management workflows.
HALO – Image Analysis Platform (简体中文 Simplified Chinese)
Download our HALO brochure in simplified Chinese 简体中文 to learn about the features and benefits of the gold standard image analysis platform for quantitative tissue analysis in digital pathology.
HALO – Image Analysis Platform (日本 Japanese)
Download our HALO brochure in 日本 Japanese to learn about the features and benefits of the gold standard image analysis platform for quantitative tissue analysis in digital pathology.
HALO, HALO AI, & HALO Link Cloud Services Brochure
Discover how our Cloud Services team can provide a secure, scalable, and flexible cloud deployment of HALO, HALO AI, and HALO Link.
HALO in the Cloud at the University of Washington
Read this case study to learn how partnering with our Cloud Services team has delivered greater scalability and cost efficiency for the BioRepository and Integrated Neuropathology laboratory at University of Washington Medicine.
NCI Case Study
Download this case study to learn about considerations the National Cancer Institute made when planning to migrate its HALO, HALO AI, and HALO Link deployments to the cloud, and benefits the NCI experienced after migration, including 50% faster HALO image analysis.
Cloud Services and AI Diagnostics Case Study
Learn how the optimized, scalable infrastructure provided by Indica Labs Cloud Services enables the rapid development and robust collaboration of our AI Diagnostics group, powering the next generation of automated AI-based decision support tools.
Clustering Workflow eBook
Check out our collaborative eBook with Lunaphore to learn about an optimized workflow for extracting information from hyperplex datasets and illuminating changes in cellular neighborhoods using HALO, HALO AI, and the Lunaphore COMET platform.
Lunaphore COMET Hyperplex IF and HALO® Image Analysis eBook
Our collaborative eBook with Lunaphore shows how HALO and HALO AI, alongside the Lunaphore COMET instrument, enable a high-throughput workflow for phenotypic and spatial analysis of cells in the tumor microenvironment.
Sequential Same Slide mIF and H&E eBook
Reveal more data on a single slide with this workflow for sequential same slide multiplex IF and H&E staining and imaging using HALO and HALO AI.
mIF Co-Registration and Cellular Analysis eBook
Learn how HALO offers a streamlined workflow for co-registration and cellular analysis of immunofluorescence images from cyclically stained and imaged slides.
Qualitative and Quantitative Evaluation of the TME eBook
Check out this ebook to see how AI-based nuclear segmentation and tissue classification can streamline cell phenotyping across tissue compartments and samples.
Identifying Immune Cell Phenotypes with RNAscope and HALO Image Analysis
Download our collaborative poster with ACD, a Bio-Techne Brand, on immune cell characterization using high-throughput spatial multiomics.
HCR™ Pro RNA-ISH Image Analysis Using HALO
Download our collaborative poster with Molecular Instruments to learn how membrane image analysis improved RNA-ISH quantification.
Characterizing the TME of a Colorectal Adenocarcinoma Sample with the Orion Spatial Biology Platform and HALO Image Analysis
Download our collaborative poster with RareCyte to learn how to analyze a colorectal adenocarcinoma sample with HALO and HALO AI
Lunaphore COMET Hyperplex IF and HALO® Image Analysis of the TME
Download our collaborative poster with Lunaphore to see how HALO and HALO AI, alongside the Lunaphore COMET instrument, enable a high throughput workflow for phenotypic and spatial analysis of cells in the tumor microenvironment.
Clustering Workflow for Advanced Cell Phenotyping of Hyperplex IF Images
Spatial Characterization of the TME with Cell DIVE Multiplexed Imaging and HALO Image Analysis
Quantitative Image Analysis of a Combined FISH-IF Assay
Characterizing the TME Using IMC and HALO Image Analysis
Automated Tumor Budding Quantification in Colorectal Carcinoma H&E Images
Spatial Multiplex Profiling of Immune Markers with the RNAscope Hiplex v2 Assay
Evaluation of the TME by High Resolution 17-plex IF and HALO Image Analysis
Our customers are making vital discoveries in oncology, neuroscience, and diabetes research. Check out some of the research our customers are publishing using the HALO Image Analysis Platform and Indica analysis modules.
HALO® High Impact Publications
Learn how HALO image analysis is leveraged in fields from immuno-oncology to neuroscience and infectious disease in this selection of high-impact publications.
RNAscope™ and HALO® Publications
Read this publications list for examples of research in areas from neuroscience to oncology using HALO to analyze RNAscope™ images.
Fetal growth restriction (FGR) is a significant concern in obstetrics, affecting 5–10% of pregnancies globally. FGR is a major contributor to perinatal morbidity and mortality and poses a significant maternal risk due to potential co-occurrence with pre-eclampsia. Despite their impact,...
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SARS-CoV-2, the causative agent of COVID-19, has been the focus of intense research since its detection in late 2019. It is known that viral infection affects several cellular processes, including senescence and inflammation, and prior studies also point toward SARS-CoV-2...
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Schwannomas are sporadic, usually benign tumors that develop predominately on spinal nerve roots and cranial nerves. Inactivation of NF2 in Schwann cells (SC) is the cause of nearly all schwannomas and mutations in additional genes are few if present at...
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Quantitative RNAscope™ Image Analysis Guide
From experimental design considerations to optimized setup of HALO image analysis parameters, our guide will help take your quantitative RNAscope™ image analysis to the next level.
Quantitative Multiplex Chromogenic Image Analysis Guide
From stain and chromogen selection to honing nuclear and membrane detection in HALO, this comprehensive guide provides best practices and optimization techniques to help take your multiplex chromogenic image analysis to the next level.
Getting Started with Multiplex Fluorescence Image Analysis in HALO®
11 June 2025 | Learn the basics of multiplex fluorescence image analysis!
Getting Started with In Situ Hybridization in HALO®
22 May 2025 | Learn the basics of in situ hybridization image analysis!
Masterclass: High Dimensional Analysis in HALO®
10 April 2025 | Learn about workflows for highly multiplexed image analysis, including in the new HALO High Dimensional Analysis module!
Getting Started with Brightfield Image Analysis in HALO®
3 April 2025 | Join us for an introductory webinar on brightfield image analysis in HALO®, designed for beginners. We’ll walk through key digital pathology
Indica Labs’ Pharma Services Launches GCP-Compliant Image Analysis Service
Albuquerque, NM, July 8, 2025 – Indica Labs, the global leader in AI-powered digital pathology software and services, today announces that their Pharma Services team
Indica Labs Announces Launch of High Dimensional Analysis Module for the HALO® Image Analysis Platform
Albuquerque, NM, 8 April 2025 – Indica Labs today announces the launch of the High Dimensional Analysis module for the HALO® image analysis platform. This
Indica Labs Joins the AWS Partner Network
Albuquerque, NM, December 4, 2024 – Indica Labs, the global leader in AI-powered digital pathology software and services, announced today that they have joined the
The Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP) Selects Indica Labs’ HALO AP® to Deliver AI-enabled Diagnostics
Albuquerque, NM, October 30, 2024 – The Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), among the leading institutes for clinical
Clearly Visualize Digital Pathology Images with View Settings Adjustments and the Figure Maker Tool
In this blog we’ll explore these platforms’ tools for view settings adjustment for fluorescent images and the integrated Figure Maker tool. Together, these features equip
Unlocking Deeper Insights with the HALO® High Dimensional Analysis Module
Extracting biological insights from highly multiplexed data requires both powerful image analysis tools and intuitive methods to navigate high-dimensional data. In this blog, we’ll cover
HALO®, HALO AI, and HALO Link 4.1 Features and Functionalities
In this blog post, you can learn about some of the new features in the 4.1 release including the new High Dimensional Analysis module, when
Open Pathology and AI Integrations: Empowering Labs with Choice
In digital pathology, advancements and proliferation in artificial intelligence (AI) and digital laboratory equipment are enabling streamlined workflows and new insights. However, they can also
Indica Labs’ Boston HALO® User Group Meeting
15 May 2025 | Indica Labs is pleased to announce our Boston HALO® User Group Meeting at Le Méridien Boston Cambridge on May 15 from
Indica Labs’ London HALO® User Group Meeting 2024
10 December 2024 | Indica Labs is pleased to announce our London HALO User Group Meeting to be held in London on 10 December 2024
Curious to Learn More About HALO AI?
With the addition of HALO AI to your HALO deployment, more AI-based features are available, enabling you to rapidly annotate images with an AI-powered annotation tool, train and optimize a variety of HALO AI classifiers, leverage validation workflows, create chained classifier pipelines, and more.
Once AI-based classifiers and phenotypers have been created with HALO AI, you can then integrate them directly into image analysis workflows with HALO modules.
Want to Learn More?
Fill out the form below to request a recorded or live demo of HALO or any of our other products or services.
You can also drop us an email at info@indicalab.com
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