Advancing Discovery with Trainable AI

Insightful and robust AI creation for pathology

Neural Network Driven Tissue and Cell Classification for Research & Routine Pathology

HALO AI is a collection of train-by-example classification and segmentation tools underpinned by advanced deep learning neural network algorithms. HALO AI classifiers can be trained to quantify tissue classes, to segment tissue classes for analysis with other HALO image analysis modules, to find rare events or cells in tissues, and to categorize cell populations into specific phenotypes.

 

Simple & Intuitive Workflow

HALO AI is fully integrated with the intuitive, easy-to-use HALO and HALO Link viewers and employs a simple three-step workflow.  After defining what tissue classes or cell phenotypes you would like to segment, you train the neural network by drawing annotations – no computer programming or AI knowledge required.  Trained classifiers can be applied to segment tissue and cells on any whole slide image or region of interest.

Powerful Tissue Segmentation

HALO AI now includes the option of three powerful neural networks – VGG, DenseNet and MiniNet. VGG, a well known and more traditional network, was used to build the Indica Labs submission in the CAMELYON17 challenge and was the first neural network integrated with HALO AI. DenseNet is a more modern network capable of creating more robust classifiers at higher resolution compared to VGG. MiniNet, a custom network developed at Indica Labs, is more shallow than VGG or DenseNet, but can produce a solution quickly with limited training data and is therefore useful for testing new AI applications. Skip down to see some applications tested with our built-in networks.

Exceptional Cell Classification

Segment nuclei with the nuclei Segmentation classifier. Utilize HALO AI’s pretrained networks for H&E, single IHC, or DAPI stained images for an out of the box solution. Or train your own nuclei segmentation network for a specific application (unique tissue or advanced staining protocols). Once nuclei are segmented, take it a step further using the Nuclei Phenotyper classifier to automatically assign cells into user defined phenotypes with a few quick training examples. Keep scrolling to see some applications tested with our Nuclei Segmentor and Nuclei Phenotyper.

HALO AI Collaboration

Want to work with external pathologists or translational research groups on a HALO AI project? No problem. Our browser-based image management system, HALO Link, is fully integrated with HALO AI to facilitate this collaboration. Once you’ve invited your collaborator to a HALO AI project, they can upload their own images and draw training annotations, nothing required except internet access and a browser. 

Request a demonstration of HALO Link using the form below or send your request by email to info@indicalab.com.

Platform Compatibility

HALO AI is compatible with all of the file formats that can be used in HALO and HALO Link. 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 AI in action on up to three of your images with a free analysis.

What Our Customers Have to Say

Read independent SelectScience reviews on our HALO AI Deep Learning Classifier Add-on and learn how these customers are using Indica Labs’ solutions to streamline their workflows.

Wonderful products, it is far beyond our expectations.

"Our lab both have the HALO Image Analysis System and the HALO AI, honestly speaking, the HALO system is beyond our expectations, especially the analysis process, annotation tools, the adjustable parameters, the texture and morphological recognition of nuclear and specific structure, and the after-sale care I strongly recommend you guys to choose it. it really worth the money."

lanlan Li

Panovue

Great results, can't live without this instrument!

"Scientists can achieve lots of high-quality analysis data about figures by HALO software. Many functions of HALO are very helpful to study images, such as TMA, spatial analysis, high-Plex FL, and especially HALO AI. It is easy to operate. Its interface is simple, friendly, and convenient. Once we have problems, a Halo technician is able to help us to solve them in time."

Junfeng Hao

Institute of Biophysics, Chinese Academy of Sciences

Great result. Nice tool for translational pathology research. 

"We are interested in applying HALO AI in RNAscope and IHC analysis. Thanks to Yongtian ZHAO to give us wonderful training and support. We are improving and confident to apply it in the RNAscope assay development and scoring."

Fei Yang

Johnson and Johnson

Currently the best image viewer and analysis software on the market that I've used.

Nathan Aleynick

MSKCC

Knowledge Center

Learn more about HALO AI image analysis by exploring the tabs below.

Characterizing the Cellular Architecture of the Tumor Microenvironment Using Imaging Mass Cytometry and Digital Image Analysis with the HALO® and HALO AI Platform

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.

Glomeruli Application Note​

Don’t let varied stain selections hold back your digital image analysis of kidney sections! With HALO AI you can develop a tissue classifier that accurately detects and segments glomeruli in sections across a range of stains including H&E, trichrome, PAMS, and DAB with hematoxylin.

HiPlex RNAscope™ Application Note

Using our FISH module we demonstrate how to perform 12-plex RNAscope image analysis using ACD’s HiPlexv2 assay.

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 based on ACD Bio’s recommended scoring guidelines.

Identifying Islets with HALO AI

Learn how HALO AI can detect islets of variable morphology in H&E-stained pancreatic tissue

Camelyon 17 Application Note​

CAMELYON17 challenged teams to develop automated methods for identifying and staging breast cancer metastases; read how the performance of a HALO AI classifier stood out among commercial entries!

HALO and HALO Link NCI Enterprise Cloud Deployment ​

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.

Sequential Same Slide Multiplex IF and H&E Staining for Combined Phenotypic and Morphological Characterization of FFPE Tissue Sections

Reveal more data on a single slide with this workflow for sequential same slide fluorescence and H&E staining and imaging using HALO and HALO AI.

Qualitative and Quantitative Evaluation of the Tissue Micro-Environment by High-Resolution 17-Plex Immunofluorescence Reveals Distinct Populations

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 eBook

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.

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.

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.

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.

Characterizing the TME using IMC and HALO® Image Analysis

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.

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.

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.

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.

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 AI Deep Learning Classifier Add-on.

HALO AI High Impact Publications

Review this selection of high-impact publications for examples of HALO AI applications in fields ranging from metabolism to immuno-oncology and myology.

HALO AI White Paper

Check out this white paper for an in-depth introduction to the deep learning-based add-on to HALO, including available networks, common functions, and the “train – validate – test” Validation workflow.

HALO Link Pharma Services White Paper

Download our white paper to learn how Indica Labs’ Pharma Services collaborates with customers and delivers HALO and HALO AI image analysis using HALO Link.

Quantitative RNAscope® Image Analysis Guide

From experimental design considerations to optimized setup of HALO and HALO AI 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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Literature

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

Camelyon 17 Application Note

CAMELYON17 challenged teams to develop automated methods for identifying and staging breast cancer metastases; read how the performance of a HALO AI classifier stood out among commercial entries!

Glomeruli Application Note

Don’t let varied stain selections hold back your digital image analysis of kidney sections! With HALO AI you can develop a tissue classifier that accurately detects and segments glomeruli in sections across a range of stains including H&E, trichrome, PAMS, and DAB with hematoxylin.

HALO Prostate AI

HALO Prostate AI offers pathologists a CE-IVD certified deep learning-based tool that can reduce turnaround times while demonstrating negative predictive values of 99% or greater in validation studies.

HALO AI High Impact Publications

Review this selection of high-impact publications for examples of HALO AI applications in fields ranging from metabolism to immuno-oncology and myology.

Sequential same slide mIF and H&E eBook

Reveal more data on a single slide with this workflow for sequential same slide fluorescence and H&E staining and imaging using HALO and HALO AI.

Qualitative and quantitative evaluation of 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.

HALO AI White Paper

Check out this white paper for an in-depth introduction to the deep learning-based add-on to HALO, including available networks, common functions, and the “train – validate – test” Validation workflow.

HALO and HALO Link NCI Enterprise Cloud Deployment

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.

Publication Spotlight

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 AI Deep Learning Classifier Add-on.

Prognostic Value of CD8+ Lymphocytes in Hepatocellular Carcinoma and Perineoplastic Parenchyma Assessed by Interface Density Profiles in Liver Resection Samples

This study examined CD8+ cell distribution in hepatocellular carcinoma (HCC) and peritumoral liver tissue to investigate the overall survival (OS) and recurrence-free survival (RFS). It is well understood that CD8+ lymphocytes are involved in both the anti-tumor response and in...

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Polycomb deficiency drives a FOXP2-high aggressive state targetable by epigenetic inhibitors

EZH2 is the catalytic component of Polycomb Repressive Complex 2 (PRC2) and performs trimethylation of histone H3 at lysine 27 (H3K27me3) to silence chromatin. PRC2 is known to play different roles in different cancers and inhibitors of PRC2 histone methyltransferase...

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Multimodal integration of radiology, pathology and genomics for prediction of response to PD-(L)1 blockade in patients with non-small cell lung cancer

Predictive biomarkers to determine which non small cell lung cancer (NSCLC) patients will respond to immunotherapy are currently lacking. In this Nature Cancer publication, the authors combine computed tomography imaging, PD-L1 immunohistochemistry (IHC), and genomic data to predict responses to...

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More Resources

Intro to the HALO AI Toolbox

Webinar

Learn about each of the HALO AI networks and their applications

Indica Labs Launches Comprehensive Management Service for HALO® Software in AWS Cloud-Hosted Environments

Press Release

Indica Labs offers AWS-hosted deployments of life science HALO software, including HALO, HALO AI, and HALO Link, as well as deployments of the clinical HALO AP platform

Neurobiology Image Analysis with HALO® and HALO AI

Webinar

Learn how to maximize utility of the new Microglial and Object Colocalization modules and how HALO AI can advance neurobiology image analysis.

Deploy HALO® and HALO AI in a Fully Managed Cloud-Hosted Environment

Indica Labs offers optimized deployments of HALO and HALO AI software hosted in Amazon Web Services (AWS). We manage all aspects of implementation and ongoing maintenance to provide a highly performant, scalable, and secure AI-enabled 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.

Want to Learn More?

Fill out the form below to request a recorded or live demo of HALO AI or any of our other products or services.
You can also drop us an email at info@indicalab.com

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