HALO

HALO® is a quantitative image analysis platform developed by Indica Labs, designed for high-throughput tissue analysis in research, pharmaceutical, and healthcare settings. Used by organizations worldwide, HALO combines unmatched ease-of-use with powerful analytic capabilities and the fastest processing speeds available in digital pathology, making it suitable for analysts at all experience levels — from those with no prior image analysis background to expert pathologists and scientists.

The platform's modular architecture allows users to start with core functionality and expand as their needs evolve. HALO reports morphological and multiplexed expression data on a cell-by-cell basis across entire tissue sections, maintaining an interactive link between cell data and the underlying image. With over 2,000 peer-reviewed publications citing HALO image analysis — spanning oncology, immuno-oncology, neuroscience, metabolism, immunology, and infectious disease — HALO has established itself as a trusted standard in quantitative pathology research.

Core Platform Capabilities

• Cell-by-cell reporting of morphological and multiplexed expression data across entire tissue sections
• Sort and filter millions of cells while visually assessing populations in the context of tissue architecture
• Interactive markup images to explore colocalization and combined phenotypes
• Pre-trained deep-learning networks for AI-powered nuclear and membrane segmentation in both brightfield and fluorescence modes
• Real-time tuning feature providing live feedback on image analysis parameters for rapid optimization
• Streamlined phenotype editor with an intuitive grid interface for assigning channel combinations and visualizing phenotypes
• Customizable analysis outputs and calculations configurable prior to running analysis
• Built-in heatmap function for spatial insights, including immune cell density surrounding tumors
• Batch analysis using saved settings, allowing automated analysis to run in the background while users continue working
• Image registration for serial IHC-stained sections with synchronized navigation
• Figure maker tool for generating publication-quality figures with control over frames, scale bars, labels, and resolution
• Advanced data export options including annotations, analysis settings, summary data, object data in spreadsheet or FCS format, and more
• Annotation tools including freehand, multi-select, and reticle-based tools, with distance measurement and snapshot capabilities
• Fluorescent image visualization with channel histogram comparison, intensity tracking, autofit calculation, and batch settings application

Available Modules and Add-Ons

• Highplex FL: Quantify expression of an unlimited number of biomarkers in any cellular compartment — membrane, nucleus, or cytoplasm — in fluorescence
• Multiplex IHC: Quantify expression of up to five brightfield stains in any cellular compartment
• High Dimensional Analysis Module: Acquire deeper insights into complex datasets using dimensional reduction and unsupervised clustering with interactive plotting
• Spatial Analysis: Plot cells and objects from one or more images and perform nearest neighbor analysis, proximity analysis, and tumor infiltration analysis
• FISH-IF: Simultaneously analyze an unlimited number of fluorescently-labeled DNA/RNA ISH probes and immunofluorescent protein biomarkers on a cell-by-cell basis
• ISH: Simultaneously analyze up to three chromogenic and/or silver-labelled DNA or RNA ISH probes on a cell-by-cell basis, measuring spot numbers, area per cell and compartment, and calculated H-scores
• ISH-IHC: Simultaneously analyze a nuclear stain and up to four IHC biomarkers or ISH probes on a cell-by-cell basis across brightfield images
• FISH: Simultaneously analyze an unlimited number of fluorescent nucleic acid probes on a cell-by-cell basis with spot numbers, area, and H-score calculations
• Tissue Classifier Add-on: Separate multiple tissue classes using a learn-by-example approach, compatible with all fluorescent and brightfield modules
• Serial Section Analysis Add-on: Develop tissue classifiers on one image and apply them across registered serial sections

Workflow and Licensing Options

1. Choose from analysis and workflow modules tailored to your research needs
2. Select a license type — single seat, multiple seat, or enterprise
3. Choose an annual or permanent license term
4. Select a deployment model — local workstation, server-based, cloud deployment managed by your team, or Indica Labs Cloud Services

Supported File Formats

• Non-proprietary formats: 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)

Training, Support, and Integrations

• Unlimited IT support, scientific support, training, and access to the Learning Portal included with every license at no additional cost
• Support staff located in the US, UK, EU, China, and Japan for coverage across all time zones
• Seamless integration with HALO AI (deep learning toolbox), HALO Link (study-based image management), and HALO AP® (case-based image management)
• Custom integrations with third-party image management systems available via an open GraphQL API
• Multi-core processing and batch analysis tools for high-throughput productivity
• Workflow tools for efficient tissue microarray and serial stain analysis

HALO is deployable on standalone workstations, server-based licenses, or cloud environments including AWS, and supports enterprise-wide rollout. Its highly interoperable ecosystem, broad file format compatibility, and open API make it adaptable to diverse laboratory IT environments and imaging instrument ecosystems.