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.

Browse our HALO modules and add-ons

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.

Before After

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.​

Learn more about our Cloud Services offering.

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 1,000 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)
  • 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

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.

Annotate and explore images with a variety of freehand tools, reticle-based tools, toggle markup images, explore intensity data, measure distances, or take a quick snapshot.​
The powerful real-time tuning feature of HALO provides live feedback on image analysis parameters.

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.

Navigate back and forth between the cell-by-cell data and the image markup with ease to explore cell populations of interest in the context of the tissue architecture. Sort cells according to biomarker intensity and immediately locate cells with highest intensity in the image, examine particular phenotypes of interest, and more.​
​Gain spatial insights with the built-in heat map function of HALO. Explore the density of immune cells surrounding a tumor or investigate the density of any other population of interest.
With the advanced export feature of HALO, you can customize an export to provide exactly the data you need for downstream analysis. Options include exporting annotations, analysis or classifier settings, reports, summary data, object data in a spreadsheet or FCS format, and more.​
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.​
Register serial IHC-stained sections in HALO and synchronize navigation to explore image analysis results. Interested in developing a tissue classifier on one image and applying it on the rest? Learn more about our Serial Section Analysis Add-on tool.
Acquire publication quality figures in just a few clicks with the figure maker feature. Quickly define the number of frames, select images of interest, then optimize scale bars, labels, fonts, opacity, and more. Save at your desired image size and resolution as a .png, .tif, or .jpg.​

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.

AllCell-Based AnalysisObject Based AnalysisArea-Based AnalysisBrightfieldFluorescentMultiplexingOncology and Immuno-OncologyRNAscopeNeuroscienceMetabolismHALO Workflow Add-On
Multiplex IHC

Quantify expression of up to five brightfield stains in any cellular compartment - membrane, nucleus or cytoplasm.

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Highplex FL

Quantify expression of an unlimited number of biomarkers in any cellular compartment - membrane, nucleus or cytoplasm.

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Tissue Classifier Add-on

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.

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Spatial Analysis

Plot cells and objects from one or more images and perform nearest neighbor analysis, proximity analysis, and tumor infiltration analysis.

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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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ISH-IHC (RNAscope™)

Quantify IHC positivity and spot number, optical density and co-expression of one or two brightfield RNA or DNA probes on a per cell basis. Includes support for brightfield RNAscope assays.

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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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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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TMA (Tissue Microarray) Add-On

Module to assist in the segmentation of TMA spots for further analysis.

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What 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.

HALO has become a fundamental tool in our research activity.

"Our Lab (Tumor Immunology Laboratory, University of Palermo) investigates immune responses in cancer. We adopted several tools for quantitative assessment of immunolabeling with good results. HALO offers high-quality cell segmentation and allows accurate analysis of both brighfield and fluorescence-based microphotographs or slide scans. The possibility to easily extract cell features integrating spatial information enables detailed spatial interaction analyses."

Claudio Tripodo

University of Palermo, Tumor Immunology Laboratory

Excellent results, easy to use and flexible. A must-have for my work!

"Easy-to-use software, interactive and well-designed. Halo software is a must-have for our research for several years. Frequent update give more and more possibility to analyze our images. And let's not forget the incredible work and reactivity of all the people in indica labs helping us when we have some trouble to optimize our algorithm. They saved us a lot of time with at a speed I have never seen elsewhere!"


Cordeliers Research Center

HALO is a user-friendly & powerful tool for image analysis w/ great technical support

"HALO is extremely straight forward and easy to use. Great and useful features include: 1. The real-time tuning tool to allow a live view of the effects of various analysis parameters for easy optimization. 2. Annotation tools make it easy to select regions of interest. 3. The ability to perform batch analysis on many images at once. 4. Useful and handy multi-panel figure maker that makes it easy for publication."

Joey Orpilla


Could not survive without this software

"HALO is user-friendly, and invaluable for quantitation of multi-omics imaging data (MIBI, CODEX/Akoya multiplex stains, RNA-ISH/RNAscope). Cell segmentation, quantitation of tissue microarray data, aligning serial images, exporting quantitative data and .fcs files, it is incredible. The support team is incredibly responsive and collaborative. HALO is a bit expensive, but it has been completely worth it for us, and it was a worthwhile investment. Highly recommend a detailed demo and purchasing this software if you are interested in quantitative data from tissue multi-omics."

Michael Kattah


Excellent replacement for older immunohistochemistry analysis software

"The software is modular and can be run on a server. This helps to increase the analysis power and while reducing the hardware requirement to do the analysis from individual's side. It accepts multiple image formats for analysis which is a plus. The representatives were professional and helped in setting up more modules with ease. Since we have used other software, migrating to this one was easy and has few more analysis set up which was useful and increased its value among our researchers."

Muralidharan Jayaraman

University of Oklahoma Health Sciences Center

We use HALO & HALO-Link daily to coordinate studies for our analysts and pathologists.

"HALO is a whole-slide image analysis platform that is designed to work how pathologists classify & score images using a microscope. It uses a set of tools that are very familiar to anyone who has used any type of image viewing/editing program at home. It can be learned in a day to analyze brightfield & fluorescent whole slide images and TMAs. There are sophisticated tools to analyze tissues labeled by chromogenic and fluorescent IHC, RNAScope, FISH & ISH. HALO may be installed on stand-alone workstations or cloud services such as AWS. File sharing through HALO-Link lets user access studies through a simple web-interface sharing a common database. HALO AI allows any user to developing sophisticated AI based tissue classification without the need for external programs or expensive computing hardware."

Timothy Baradet

Bristol-Myers Squibb

For the Pathologist HALO is by far the best digital image analysis platform available.

"As a Pathologist specializing in digital image analysis, I have had the opportunity to use several different digital image analysis platforms. Indica Labs' HALO is by far the most accurate, versatile and user friendly digital image analysis platform that I have used. Literally within 10-15 minutes of "tuning" one of their "out of the box" detection algorithms, I can perform image analysis for most simple immunohistochemical markers. The workflow is simple, with sacanned images being imported directly into HALO with or without annotations for analysis. This even allows for remote use when working off site. The customer support is AMAZING and I routinely get same day or next day help from the technical support reps. HALO is a must have for any pathologist or scientist involved in quantifying immunohistochemical stains. In addition the HALO AI module is extremely easy to use. Within 20 minutes I was able to set up AI detection of tumor vs. normal tissue, as well as tumor epithelium vs. stroma. HALO provides everything one needs for quantification of IHC for clinical and pre-clinical studies (of course with supervision of a pathologist). Best of all: it is fun, like a video game for Pathologists!"

Philip Martin


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.

Imaging Mass Cytometry Application Note

See in this app note how automated analysis of highly multiplexed IMC images using HALO® and HALO AI yields rich cellular and spatial data from a streamlined workflow.

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 and 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.

Quantify Single and Multiplexed RNAscope® Probes Across Whole Slide Tissues

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 Brochure

Download our HALO brochure 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 (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. 

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.

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.

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

Download our collaborative poster with Lunaphore to learn about a clustering workflow that uses unsupervised learning for COMET™ images.

Spatial Characterization of the TME with Cell DIVE Multiplexed Imaging and HALO Image Analysis

Check out our collaborative poster with Cell Signaling Technology and Leica Microsystems to learn about a combined workflow for spatial analysis of the TME.

Quantitative Image Analysis of a Combined FISH-IF Assay

Learn how to detect protein and RNA in a single assay using ACD’s Co-Detection workflow and HALO image analysis.

Characterizing the TME Using IMC and HALO Image Analysis

Download this poster to learn how HALO and HALO AI can be used to analyze imaging mass cytometry data.

Automated Tumor Budding Quantification in Colorectal Carcinoma H&E Images

Learn about quantification of tumor budding in colorectal carcinoma using HALO and HALO AI.

Spatial Multiplex Profiling of Immune Markers with the RNAscope Hiplex v2 Assay

Download this poster to learn about combining ACD’s HiPlex v2 in situ hybridization assay with HALO image analysis.

Evaluation of the TME by High Resolution 17-plex IF and HALO Image Analysis

Learn how to perform highly multiplexed IF and image analysis using the Orion instrument combined with HALO and HALO AI 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.

SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence

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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Cellular mechanisms of heterogeneity in NF2-mutant schwannoma

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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Modulation of the Human Pancreatic Ductal Adenocarcinoma Immune Microenvironment by Stereotactic Body Radiotherapy

Stereotactic body radiotherapy (SBRT) uses multiple targeted beams of radiation to damage malignant cells while limiting effects to surrounding tissue. SBRT is a standard treatment for various cancers that elicit strong immune responses, but immunologically cold tumors, such as pancreatic...

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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.

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.