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HALO® Module

FISH-IF Quantification

(Designed for RNAscope®)

Indica Labs FISH-IF quantification module measures any number of fluorescently-labeled DNA/RNA ISH probes and immunofluorescent (IF) protein biomarkers on a cell-by-cell basis. This allows the user to rapidly contextualize the corresponding protein and gene expression profile of every cell across the tissue. HALO® FISH-IF analysis is designed to work with an unlimited number of fluorescent protein biomarkers and probes.

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.

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!

Title Authors Year Journal Application HALO Modules Product
Detection of EpsteinñBarr 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
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
Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders Eroglu E, Yen C, Witman N, Elewa A, Araus A, Wang H, Szattler T, Umeano C, Sohlmer J, Goedel A, Simon A, Chien K 2022 Nature Cell Biology Myology ISH/FISH, 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
Systemic Nos2 Depletion and Cox inhibition limits TNBC disease progression and alters lymphoid cell spatial orientation and density Somasundaram 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 D 2022 Redox Biology Oncology Classifer, ISH/FISH, Spatial Analysis, Registration, 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 Spatial Analysis, ISH-IHC/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
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
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
The potassium channel auxiliary subunit Kv_2 (Kcnab2) regulates Kv1 channels and dopamine neuron firing Yee J, Rastani A, Soden M 2022 Journal of Neurophysiology Neuroscience ISH-IHC/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
Exploration of spatial heterogeneity of tumor microenvironment in nasopharyngeal carcinoma via transcriptional digital spatial profiling Wang L, Wang D, Zeng X, Zhang Q, Wu H, Liu J, Wang Y, Liu G, Poan Y 2023 International Journal of Biological Sciences Oncology Area Quantification, ISH-IHC/FISH-IF HALO

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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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.

Learn More
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.

Learn More

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