Before Markup

FISH-IF Module

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)
  • DICOM (DCM*)
    *whole-slide images

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.

RNAscope® Publications with the HALO® Image Analysis Platform

Read this publications list to see 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.

Publication Spotlight

The table below includes publications that cite the FISH-IF and ISH-IHC modules. 

Your publication not on the list?  Drop us an email to let us know about it!

TitleAuthorsYearJournalApplicationHALO ModulesProduct
Detection of EpsteinñBarr Virus in Periodontitis: A Review of Methodological ApproachesTonoyan L, Chevalier M, Vincent-Bungnas S, Marsault R, Doglio A2021MircroorganismsReviewISH/FISH, ISH-IHC/FISH-IFHALO
Detection of engineered T cells in FFPE tissue by multiplex in situ hybridization and immunohistochemistryWright 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 RH2020Journal of Immunological MethodsImmunologyISH/FISH, ISH-IHC/FISH-IFHALO
Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamandersEroglu E, Yen C, Witman N, Elewa A, Araus A, Wang H, Szattler T, Umeano C, Sohlmer J, Goedel A, Simon A, Chien K2022Nature Cell BiologyMyologyISH/FISH, ISH-IHC/FISH-IFHALO
Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor immunosuppressive phenotypePorter 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 D2022The Journal of Clinical InvestigationImmuno-oncologyISH/FISH, ISH-IHC/FISH-IFHALO
Systemic Nos2 Depletion and Cox inhibition limits TNBC disease progression and alters lymphoid cell spatial orientation and densitySomasundaram V, Ridnour L, Cheng R, Walke A, Kedei N, Bhattacharyya D, Wink A, Edmondson E, Butcher D, Warner A, Dorsey T, Scheiblin D, Heinz W, Bryant R, Kinders R, Lipkowitz S, Wong S, Pore M, Hewitt S, McVicar D, Anderson S, Chang J, Glynn S, Ambs S, Lockett S, Wink D2022Redox BiologyOncologyClassifer, ISH/FISH, Spatial Analysis, Registration, ISH-IHC/FISH-IFHALO
Annexin A2/TLR2/MYD88 pathway induces arginase 1 expression in tumor-associated neutrophilsZhang H, Zhu X, Friesen T, Kwak J, Pisarenko T, Mekvanich S, Velasco M, Randolph T, Kargl J, Houghton A2022Journal of Clinical InvestigationImmuno-oncologySpatial Analysis, ISH-IHC/FISH-IFHALO
Spatiotemporal transcriptome analysis reveals critical roles for mechano-sensing genes at the border zone in remodeling after myocardial infarctionYamada 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 I2022Nature Cardiovascular ResearchMyologyISH-IHC/FISH-IFHALO
Loss of functional System x-c uncouples aberrant postnatal neurogenesis from epileptogenesis in the hippocampus of Kcna1-KO miceAloi M, Thompson S, Quartapella N, Noebels J2022Cell ReportsNeuroscienceISH-IHC/FISH-IFHALO
Multiparameter immunohistochemistry analysis of HIV DNA, RNA and immune checkpoints in lymph node tissueRichardson 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 P2021Journal of Immunological MethodsInfectious DiseaseISH-IHC/FISH-IFHALO
The potassium channel auxiliary subunit Kv_2 (Kcnab2) regulates Kv1 channels and dopamine neuron firingYee J, Rastani A, Soden M2022Journal of NeurophysiologyNeuroscienceISH-IHC/FISH-IFHALO
Transcriptional vulnerabilities of striatal neurons in human and rodent models of Huntington’s diseaseMatsushima A, Pineda S, Crittenden J, Lee H, Galani K, Mantero J, Tombaugh G, Kellis M, Heiman M, Graybiel A2023Nature CommunicationsNeuroscienceArea Quantification, ISH-IHC/FISH-IFHALO
Exploration of spatial heterogeneity of tumor microenvironment in nasopharyngeal carcinoma via transcriptional digital spatial profilingWang L, Wang D, Zeng X, Zhang Q, Wu H, Liu J, Wang Y, Liu G, Poan Y2023International Journal of Biological SciencesOncologyArea Quantification, ISH-IHC/FISH-IFHALO

Related HALO Modules

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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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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Simultaneously analyze a nuclear stain and up to four IHC biomarkers or ISH probes on a cell-by-cell basis across brightfield images.​

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Use the arrows above to view additional related modules

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