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. This module enables in-depth analysis of the corresponding protein and gene expression profile of every cell across the tissue, with outputs including biomarker positive cells in total and by cell compartment, probe copies and area per cell, and calculated H-scores for each probe. You can optimize image analysis with available pre-trained AI-based membrane and/or nuclear segmentation, now included with the HALO platform, and leverage interactive markups to dynamically explore colocalization and combined cell phenotypes.
Try it out! Click here to initiate your free proof-of-concept HALO image analysis.
File formats supported by the HALO image analysis platform:
- Non-proprietary (JPG, TIF, OME.TIFF)
- Nikon (ND2)
- 3D Histech (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
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.
HiPlex RNAscope™ Application Note
Using our FISH module we demonstrate how to perform 12-plex RNAscope image analysis using ACD’s HiPlexv2 assay.
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.
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.
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.
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.
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.
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.
Advancing Neuroscience Research with HALO® and HALO AI
As scientists work to continue unraveling the structural, cellular, and molecular complexities of the brain and its diseases, the characteristics of this unique tissue pose
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
Interactive Markup Images: Providing a Dynamic Look at HALO® Analysis Results
At Indica Labs, our HALO platforms are optimized for ease-of-use as well as powerful, accurate analysis, and include multiple features to help users get the
Announcing HALO® Highplex FL and FISH-IF Modules Supporting AI Membrane Segmentation
In this blog post, you can learn about the AI membrane segmentation support added to the HALO® Highplex FL and FISH-IF modules, where to find
Getting Started with RNAscope™ Image Analysis in HALO®
28 March 2023 | Join us for this 1-hour webinar to see a live demonstration of RNAscope image analysis using the HALO® platform from Indica
Masterclass Webinar: Optimizing RNAscope Image Analysis
05 May 2022 | In this 60-min webinar, Dr. Ghislaine Lioux will present solutions to common RNAscope image analysis challenges including how to optimize color
Whole-slide Quantitative RNAscope Image Analysis: Applications and Methods
20 April 2022 | In this 2-hour event, learn from three experts in RNAscope image analysis with HALO® as they present their scientific research, share
HALO Image Analysis Masterclass Series: February-March 2021
Spring of 2021 | Indica Labs is excited to continue our HALO® Masterclass Webinar Series this winter. Each masterclass webinar will offer a deep dive
Publication Spotlight
The table below includes publications that cite the FISH-IF and module.
Your publication not on the list? Drop us an email to let us know about it!
| Title | Authors | Year | Journal | Topics | HALO Modules | Products |
|---|---|---|---|---|---|---|
| Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex | Huuki-Myers L A, Montgomery K D, Kwon S H, Cinquemani S, Eagles N J, Gonzalez-Padilla D, Maden S K, Kleinman J E, Hyde T M, Hicks S C, Maynard K R, Collado-Torres L | 2025 | Genome Biology | Neuroscience | FISH-IF | HALO |
| Repeated head trauma causes neuron loss and inflammation in young athletes | Butler M, Pervaiz N, Breen K, Calderazzo S, Ypsilantis P, Wang Y, Cammasola Breda J, Mazzilli S, Nicks R, Spurlock E, Hefti M, Fiock K, Huber B, Alvarez V, Stein T, Campbell J, McKee A, Cherry J | 2025 | Nature | Neuroscience | Object Colocalization, FISH, Spatial Analysis, Highplex FL, FISH-IF | HALO, HALO AI |
| A γδ T cell–IL-3 axis controls allergic responses through sensory neurons | Flayer C H, Kernin I J, Matatia P R, Zeng X, Yarmolinsky D A, Han C, Naik P R, Buttaci D R, Aderhold P A, Camire R B, Zhu X, Tirard A J, McGuire J T, Smith N P, McKimmie C S, McAlpine C S, Swirski F K, Woolf C J, Villani A C, Sokol C L | 2024 | Nature | Neuroscience | Area Quantification, FISH-IF | HALO, HALO AI |
| Cellular mechanisms of heterogeneity in NF2-mutant schwannoma | Chiasson-MacKenzie C, Vitte J, Liu C, Wright E, Flynn E, Stott S, Giovannini M, McClatchey A | 2023 | Nature Communications | Oncology | Classifier, Multiplex IHC, Spatial Analysis, FISH-IF | HALO |
| Transcriptional vulnerabilities of striatal neurons in human and rodent models of Huntington’s disease | Matsushima A, Pineda S, Crittenden J, Lee H, Galani K, Mantero J, Tombaugh G, Kellis M, Heiman M, Graybiel A | 2023 | Nature Communications | Neuroscience | Area Quantification, ISH-IHC/FISH-IF | HALO |
| Lorazepam stimulates IL-6 production and is associated with poor survival outcomes in pancreatic cancer. | Cornwell A, Tisdale A, Venkat S, Maraszek K, Alahmari A, George A, Attwood K, George M, Rempinski D, Franco-Barraza J, Parker M, Gomez E, Fountzilas C, Cukierman E, Steele N, Feigin M | 2023 | medrxiv | Oncology | FISH-IF | HALO |
| Tyrosinase-induced neuromelanin accumulation triggers rapid dysregulation and degeneration of the mouse locus coeruleus | Iannitelli A, Segal A, Pare J, Mulvey B, Liles L, Sloan S, McCann K, Dougherty J, Smith Y, Weinshenker D | 2023 | bioRxiv | Neuroscience | FISH-IF | HALO |
| Pseudoknot-targeting Cas13b combats SARSCoV-2 infection by suppressing viral replication | Yu D, Han H, Yu J, Kim J, Lee G, Yang J, Song B, Tark D, Choi B, Kang S, Heo W | 2023 | Molecular Therapy | Infectious Disease | ISH, FISH-IF | HALO |
| HIF-1 regulates pathogenic cytotoxic T cells in lupus skin disease | Little A, Chen P, Vesely M, Khan R, Fiedler J, Garritano J, Maisha F, McNiff J, Craft J | 2023 | JCI Insight | Immunology, Dermatology | FISH-IF | HALO, HALO AI |
| Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue | Huuki-Myers L, Montgomery KD, Kwon SH, Page SC, Hicks SC, Maynard KR, Collado-Torres L | 2023 | Genome Biology | Other | FISH-IF | HALO |
| Prednisolone and rapamycin reduce the plasma cell gene signature and may improve AAV gene therapy in cynomolgus macaques | Kistner A, Chichester J A, Wang L, Calcedo R, Greig J A, Cardwell L N, Wright M C, Couthouis J, Sethi S, McIntosh B E, McKeever K, Wadsworth S, Wilson J M, Kakkis E, Sullivan B A | 2023 | Gene Therapy | Other | FISH-IF | HALO |
| Entorhinal cortex vulnerability to human APP expression promotes hyperexcitability and tau pathology | Rowan M, Goettemoeller A, Banks E, McCann K, Kumar P, South K, Olah V, Ramelow C, Duong D, Seyfried N, Rangaraju S, Weinshenker D | 2023 | Research Square | Neuroscience | FISH-IF | HALO |
| High-resolution and quantitative spatial analysis reveal intra-ductal phenotypic and functional diversification in pancreatic cancer | Michiels E, Madhloum H, Lint S, Messaoudi N, Kunda R, Martens S, Giron P, Olsen C, Lefesvre P, Dusetti N, Mohajer L, Tomasini R, Hawinkels L J, Ahsayni F, Nicolle R, Arsenijevic T, Bouchart C, Laethem J L, Rooman I | 2023 | Journal of Pathology | Oncology | Spatial Analysis, FISH-IF | HALO |
| Spatiotemporal transcriptome analysis reveals critical roles for mechano-sensing genes at the border zone in remodeling after myocardial infarction | Yamada S, Ko T, Hatsuse S, Nomura S, Zhang B, Dai Z, Inoue S, Kubota M, Sawami K, Yamada T, Sassa T, Katagiri M, Fujita K, Katoh M, Ito M, Harada M, Toko H, Takeda N, Morita H, Aburatani H, Komuro I | 2022 | Nature Cardiovascular Research | Myology | ISH-IHC/FISH-IF | HALO |
| Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor immunosuppressive phenotype | Porter R, Sun S, Flores M, Berzolla E, You E, Phillips I, KC N, Desai N, Tai E, Szabolcs A, Lang E, Pankaj A, Raabe M, Thapar V, Xu K, Nieman L, Rabe D, Kolin D, Stover E, Pepin D, Stott S, Deshpande V, Liu J, Solovyov A, Matulonis U, Greenbaum B, Ting D | 2022 | The Journal of Clinical Investigation | Immuno-oncology | ISH/FISH, ISH-IHC/FISH-IF | HALO |
| Annexin A2/TLR2/MYD88 pathway induces arginase 1 expression in tumor-associated neutrophils | Zhang H, Zhu X, Friesen T, Kwak J, Pisarenko T, Mekvanich S, Velasco M, Randolph T, Kargl J, Houghton A | 2022 | Journal of Clinical Investigation | Immuno-oncology | ISH-IHC/FISH-IF | HALO |
| Loss of functional System x-c uncouples aberrant postnatal neurogenesis from epileptogenesis in the hippocampus of Kcna1-KO mice | Aloi M, Thompson S, Quartapella N, Noebels J | 2022 | Cell Reports | Neuroscience | ISH-IHC/FISH-IF | HALO |
| The potassium channel auxiliary subunit Kvβ2 (Kcnab2) regulates Kv1 channels and dopamine neuron firing | Yee J, Rastani A, Soden M | 2022 | Journal of Neurophysiology | Neuroscience | ISH-IHC/FISH-IF | HALO |
| Spatially organized multicellular immune hubs in human colorectal cancer | Pelka K, Hofree M, Chen J, Sarkizova S, Pirl J, Jorgji V, Bejnood A, Dionne D, Ge W, Xu K, Chao S, Zollinger D, Lieb D, Reeves J, Fuhrman C, Hoang M, Delorey T, Nguyen L, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers, J, Smillie C, Cuoco M, Wu J, Su M, Yeung J, Vijaykumar B, Magnuson A, Asinovski N, Moll T, Goder-Reise M, Applebaum A, Brais L, DelloStritto L, Denning S, Phillips S, Hill E, Meehan J, Frederick D, Sharova T, Kanodia A, Todres E, Jane-Valbuena J, Biton M, Izar B, Lambden C, Clancy T, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger D, Srivastava A, Hornick J, Ogino S, Rotem A, Vigneau S, Johnson B, Corcoran R, Sharpe A, Kuchroo V, Ng K, Giannakis M, Nieman L, Boland G, Arguirre A, Anderson A, Rosenblatt-Rosen O, Regev A, Hachohen N | 2021 | Cell | Oncology | Spatial Analysis, ISH-IHC/FISH-IF | HALO |
| Detection of Epstein–Barr Virus in Periodontitis: A Review of Methodological Approaches | Tonoyan L, Chevalier M, Vincent-Bungnas S, Marsault R, Doglio A | 2021 | Mircroorganisms | Review | ISH/FISH, ISH-IHC/FISH-IF | HALO |
| Multiparameter immunohistochemistry analysis of HIV DNA, RNA and immune checkpoints in lymph node tissue | Richardson Z, Deleage C, Tutuka C, Walkiewica M, Del Rio-Estrada P, Pascoe R, Evans V, Reyesteran G, Gonzales M, Roberts-Thomson S, Gonzalez-Navarro M, Torres-Ruiz, F, Estes J, Lewin S, Cameron P | 2021 | Journal of Immunological Methods | Infectious Disease | ISH-IHC/FISH-IF | HALO |
| Detection of engineered T cells in FFPE tissue by multiplex in situ hybridization and immunohistochemistry | Wright JH, Huang L-Y, Weaver S, Archila LD, McAfee MS, Hirayama AV, Chapuis AG, Bleakley M, Rongvaux A, Turtle CJ, Chanthaphavong S, Campbell JS, Pierce RH | 2020 | Journal of Immunological Methods | Immunology | ISH/FISH, ISH-IHC/FISH-IF | HALO |
Related HALO Modules
Acquire deeper insights into complex data sets using dimensional reduction and unsupervised clustering with interactive plotting.
Learn More
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.
Learn More
Simultaneously analyze a nuclear stain and up to four IHC biomarkers or ISH probes on a cell-by-cell basis across brightfield images.
Learn MoreUse the arrows above to view additional related modules
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