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, pharmaceutical, healthcare and research organizations worldwide are using HALO® for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology and more.

 

Accessible Modules and Add-ons

HALO® modules simplify the analysis workflow so there is no need to ‘build’ algorithms from scratch. Our modules make HALO easy-to-use and understand which means you can spend less time learning software and more time analyzing data.

HALO add-ons can be used in combination with any of the other analysis modules to improve the analysis workflow. These include tools to help automate tissue segmentation, such as tissue classifier, serial section analysis, and TMA, as well as tools to improve image processing speeds for high-throughput labs, such as analysis cluster.

Browse our HALO modules and add-ons.

Extensive Analytics

HALO reports morphological and multiplexed expression data on a cell-by-cell basis across entire tissue sections and maintains an interactive link between cell data and cell image. Click on any cell in the image and immediately see analysis outputs for that specific cell. Sorting and filtering capabilities allow the user to mine millions of cells while visually assessing corresponding cell populations. For example, sort cells according to biomarker intensity and immediately locate cells with highest intensity in the image. Just imagine the endless possibilities.

Scalable Platform

HALO’s modular design and flexible licensing allow it to be adapted to any requirement and budget. Start with all the modules or just a few and add more modules as your needs change. Use HALO on a single workstation or ramp up to a server-based license for your entire group. Purchase a permanent license or renew annually.

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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ISH (RNAscope™)

Quantify 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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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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FISH (RNAscope™)

Quantify number, intensity and co-expression of an unlimited number of fluorescently labeled RNA or DNA probes on a per cell basis. Includes support for fluorescent RNAscope assays.

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FISH-IF (RNAscope™)

Quantify an unlimited number of fluorescent RNA/DNA probes and IF protein biomarkers on a per cell basis. Includes support for fluorescent RNAscope assays.

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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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Platform Compatibility

HALO® is compatible with a broad spectrum of image and digital slide formats.  Yours not on the list? Email us your requirements.

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

Free Image Analysis

See HALO® image analysis in action on up to three of your images. 

What Our Customers Have to Say

Read independent SelectScience reviews on our HALO® image analysis 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!"

Yoan VELUT

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

UCLA

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

UCSF

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

AstraZeneca

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.

Quantifying Immune Cells in the Tumor Microenvironment Using HALO® Spatial Analysis Tools

Using our Multiplex IHC module, we quantify immune cells and tumor cell markers across whole slide images.  The tissue classifier add-on is employed to segment tumor and stroma and the spatial analysis module is used for proximity and invasive margin analysis. 

Fusion of Spectrally Unmixed Image Tiles from PerkinElmer® VectraTM 3 or PolarisTM into Whole Slide Tifs to Enable Analysis of the Tumor Microenvironment

We demonstrate how HALO can create a multispectral 7-plex whole slide image from individual field-of-view image tiles captured from the PerkinElmer Vectra 3 or Polaris platform and analyze these images using our Highplex FL module and spatial analysis modules.

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.

Quantify Single and Multiplexed RNAscope® Probes Across Whole Slide Tissues

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

After the National Cancer Institute migrated their HALO, HALO AI, and HALO Link deployments to the cloud, they experienced 50% faster HALO image analysis in the cloud environment! Learn about additional benefits of cloud deployment for the NCI, considerations they made when planning their deployment, and more in this case study.

Depicting TME Cellular Architecture Using Hyperplex IF and Automated Image Analysis

Read this eBook for an introduction to a sequential staining and image analysis workflow that leverages a terminal H&E stain for the delineation of tissue architectural regions in subsequent HALO image analysis.

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 Poster

Our collaborative poster 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.

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.

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.

China User Group Meeting

Indica Labs’ China User Group Meeting Date: 18 October 2023 Time: 13:30 – 17:30 Location: Evergreen Laurel Hotel – Shanghai For more information, please email china@indicalab.com.

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Top Notch Training and Support

We’ve worked hard to ensure our HALO® platform interfaces are the most intuitive in the industry, but we realize that you may still need extra support. We’ve got you covered!

Unlimited IT support, scientific support & training are included with every license at no additional cost. With support staff in the US, UK and Japan, you are supported in any time zone. Need help tuning an algorithm or training for new staff – we are just a call away.

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.

Literature

Learn more about applications of HALO® image analysis in this selection of our most popular application notes, publication lists, white papers, and more!

Quantifying Immune Cells in the Tumor Microenvironment Using HALO® Spatial Analysis Tools

Using our Multiplex IHC module, we quantify immune cells and tumor cell markers across whole slide images.  The tissue classifier add-on is employed to segment tumor and stroma and the spatial analysis module is used for proximity and invasive margin analysis. 

Fusion of Spectrally Unmixed Image Tiles from PerkinElmer® VectraTM 3 or PolarisTM into Whole Slide Tifs to Enable Analysis of the Tumor Microenvironment

We demonstrate how HALO can create a multispectral 7-plex whole slide image from individual field-of-view image tiles captured from the PerkinElmer Vectra 3 or Polaris platform and analyze these images using our Highplex FL module and spatial analysis modules.

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.

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.