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HALO® Module


(Designed for RNASCOPE®)

Indica Labs’ FISH module quantifies an unlimited number of DNA or RNA FISH probes on a cell-by-cell basis. This analysis module can be used with most multiplex RNA FISH assays including RNAscope® and supports the H-score protocol for RNAscope® recommended by the manufacturer, ACD, a Bio-techne brand.

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 RNAscope Image Analysis Guide​

Advance your RNAscope image analysis by downloading the latest Quantitative RNAscope Image Analysis Guide from Indica Labs and ACD, a Bio-techne brand.

Characterization of Immune Cell Phenotypes through Quantification of the 12-Plex Spatial RNAscope™ HiPlex v2 Assay Using the HALO® Image Analysis Platform

In this application note, we demonstrate how the HALO® image analysis platform can be employed with HiPlex v2 to (1) quantitatively assess differential expression of 12 RNA targets, (2) quantify six distinct cell phenotypes based on gene expression, and (3) analyze spatial relationships between cell phenotypes within the Tumor Microenvironment.

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.

Publication Spotlight

The table below includes publications that cite the FISH and ISH 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
EBV+†tumors exploit tumor cell-intrinsic and -extrinsic mechanisms to produce regulatory T cell-recruiting chemokines CCL17 and CCL22 Jorapur A, Marshall L, Jacobson S, Xu M, Marubayashi S, Zibinsky M, Hu D, Robles O, Jackson J, Baloche V, Busson P, Wustrow D, Brockstedt D, Talay O, Kassner P, Cutler G 2022 PLOS Pathogens Oncology ISH/FISH HALO
AAV9/MFSD8 gene therapy is effective in preclinical models of neuronal ceroid lipofuscinosis type 7 disease Chen X, Dong T, Hu Y, Shaffo F, Belur N, Mazzulli J, Gray S 2022 The Journal of Clinical Investigation Neuroscience Area Quantification, ISH/FISH HALO
Genome Sequence and Experimental Infection of Calves with Bovine Gammaherpesvirus 4 (BoHV-4) Bauermann F, Falkenberg S, Martins M, Dassanayake R, Neill J, Ridpath J, Silveira S, Palmer M, Buysse A, Mohr A, Flores E, Diel D 2022 Research Square Infectious Disease, Other ISH/FISH HALO
Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life Brand M, Proctor A, Hostetter J, Zhou N, Friedberg I, Jergens A, Phillips G, Wannemuehler M 2022 PLOS ONE Other ISH/FISH 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
TGF?1 Induces Senescence and Attenuated VEGF Production in Retinal Pericytes Avarmovic D, Archaimbault S, Kemble A, Gruener S, Lazendic M, Westenskow P 2022 Biomedicines Other ISH/FISH 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
Distinct Encoding of Reward and Aversion by Peptidergic BNST Inputs to the VTA Soden M, Yee J, Cuevas B, Rastani A, Elum J, Zweifel L 2022 Frontiers in Neural Circuits Neuroscience ISH/FISH HALO
Hyperpolarised†13C-MRI identifies the emergence of a glycolytic cell population within intermediate-risk human prostate cancer Sushentsev N, McLean M, Warren A, Benjamin A, Brodie C, Frary A, Gill A, Jones J, Kaggie J, Lamb B, Locke M, Miller J, Mills I, Priest A, Robb F, Shah N, Schulte R, Graves M, Gnanapragasam V, Brindle K, Barrett T, Gallacher F 2022 Nature Communications Oncology ISH/FISH, Membrane, Multiplex IHC HALO
Adult re-expression of IRSp53 rescues NMDA receptor function and social behavior in IRSp53-mutant mice Noh Y, Yook C, Kang J, Lee S, Kim Y, Yang E, Kim H, Kim E 2022 Communications Biology Neuroscience ISH/FISH, Figure Maker HALO
The NALCN channel regulates metastasis and nonmalignant cell dissemination Rahrmann E, Shorthouse D, Jassim A, Hu L, Ortiz M, Mahler-Araujo B, Vogel P, Paez-Ribes M, Fatemi A, Hannon G, Iyer R, Blundon J, Lourenco F, Kay J, Nazarian R, Hall B, Zakharenko S, Winton D, Zhu L, Gilbertson R 2022 Nature Genetics Oncology ISH/FISH, Multiplex IHC HALO
Relaxin/insulin-like family peptide receptor 4 (Rxfp4) expressing hypothalamic neurons Q8 modulate food intake and preference in mice Lewis J, Woodward O, Nuzzaci D, Smith C, Adriaenssens A, Billing L, Brighton C, Phillips B, Tadross J, Kinston S, Ciabatti E, Gottgens B, Tripodi M, Mornigold D, Baker D, Gribble F, Reimann F 2022 Molecular Metabolism Metabolism ISH/FISH, Highplex FL HALO
Regional epithelial cell diversity in the small intestine of pigs Wiarda J, Becker S, Sivasankaran S, Loving C, 2022 Journal of Animal Science Gastroenterology ISH/FISH, Figure Maker HALO
Single cell analysis of cribriform prostate cancer reveals cell intrinsic and tumor microenvironmental pathways of aggressive disease Wong H, Sheng Q, Hesterberg A, Croessmann S, Rios B, Giri K, Jackson J, Miranda A, Watkins E, Schaffer K, Donahue M, Winkler E, Penson D, Smith J, Herrell S, Luckenbaugh A, Barocas D, Kim Y, Graves D, Giannico G, Rathmell J, Park B, Gordetsky J, Hurley P 2022 Nature Communications Oncology ISH/FISH 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
Glutaminase 2 Knockdown Reduces Hyperammonemia and Associated Lethality of Urea Cycle Disorder Mouse Model Mao X, Chen H, Lin A, Kim S, Burczynski M, Na E, Halasz G, Sleeman M, Murphy A, Okamoto H, Cheng X 2022 Journal of Inherited Metabolic Disease Metabolism Area Quantification, ISH/FISH HALO
What Happens to the Preserved Renal Parenchyma After Clamped Partial Nephrectomy? Xiong L, Nguyen J, Peng Y, Zhou Z, Ning K, Jia N, Nie J, Wen D, Wu Z, Roversi G, Palacios D, Abramczyk E, Munoz-Lopez C, Campbell J, Cao Y, Li Wencai, Zhang X, He Z, Li X, Huang J, Shou J, Wu J, Chen M, Chen X, Zheng J, Xu C, Zhong W, Li Z, Dong W, Zhou J, Zhang H, Luo J, Liu J, Sun G, Han H, Guo S, Dong P, Zhou F, Yu C, Campbell S, Zhang Z 2022 European Urology Other Area Quantification, ISH/FISH HALO
Adolescent intermittent ethanol exposure produces Sex-Specific changes in BBB Permeability: A potential role for VEGFA Vore A, Barney T, Deak M, Varlinskaya E, Deak T 2022 Brain, Behavior, and Immunity Neuroscience ISH/FISH HALO
Relationship between impaired BMP signalling and clinical risk factors at early-stage vascular injury in the preterm infant Heydarian M, Oak P, Zhang X, Kamgari N, Kindt A, Koschlig M, Pritzke T, Gonzalez-Rodriguez E, Forster K, Morty R, Hafner F, Hubener C, Flemmer A, Yildirim A, Sudheendra D, Tian X, Petrera A, Kirsten H, Ahnert P, Morrell N, Desai T, Sucre J, Spiekerkoetter E, Hilgendorff A 2022 Thorax Other ISH/FISH HALO
Spatiotemporal expression pattern of Progesterone Receptor Component (PGRMC) 1 in endometrium from patients with or without endometriosis or adenomyosis Thieffry C, Van Wynendaele M, Samain L, Tyteca D, Pierreux C, Marbaix E, Henriet P 2022 The Journal of Steroid Biochemistry and Molecular Biology Other ISH/FISH, Highplex FL HALO, HALO AI
Quantitative Imaging Analysis of the Spatial Relationship between Antiretrovirals, Reverse Transcriptase Simian-Human Immunodeficiency Virus RNA, and Fibrosis in the Spleens of Nonhuman Primates Devanathan A, White N, Desyaterik Y, De la Cruz G, Nekorchuk M, Terry M, Busman-Sahay K, Adamson L, Luciw P, Fedoriw Y, Estes J, Rosen E, Kashuba A 2022 Antimicrobial Agents and Chemotherapy Infectious Disease ISH/FISH HALO
CD123-directed allogeneic chimeric-antigen receptor T-cell therapy (CAR-T) in blastic plasmacytoid dendritic cell neoplasm (BPDCN): Clinicopathological insights Pemmaraju N, Wilson N, Senapati J, Economides M, Guzman M, Neelapu S, Kazemimood R, Davis R, Jain N, Khoury J, Sugita M, Cai T, Smith J, Frattini M, Garton A, Roboz G, Konopleva M 2022 Leukemia Research Immuno-oncology ISH/FISH HALO
Localization of macrophage subtypes and neutrophils in the prostate tumor microenvironment and their association with prostate cancer racial disparities Maynard J, Godwin T, Lu J, Vidal I, Lotan T, De Marzo A, Joshu C, Sfanos K 2022 The Prostate Oncology ISH/FISH, Multiplex IHC HALO
Molecular identification of spatially distinct anabolic responses to mechanical loading in murine cortical bone Chlebek C, Moore J, Ross F, van der Meulen M 2022 Journal of Bone and Mineral Research Other ISH/FISH HALO
Sex-specific effects of ethanol consumption in older Fischer 344 rats on microglial dynamics and A_(1-42) accumulation Marsland P, Vore A, DaPrano E, Paluch J, Blackwell A, Varlinskaya E, Deak T 2022 Alcohol Neuroscience ISH/FISH HALO
Estrogen receptor beta activity contributes to both tumor necrosis factor alpha expression in the hypothalamic paraventricular nucleus and the resistance to hypertension following angiotensin II in female mice Woods C, Contoreggi N, Johnson M, Milner T, Wang G, Glass M, 2022 Neurochemistry International Neuroscience ISH/FISH HALO
Angiotensin II Infusion Results in Both Hypertension and Increased AMPA GluA1 Signaling in Hypothalamic Paraventricular Nucleus of Male but not Female Mice Wang G, Woods C, Johnson M, Milner T, Glass M 2022 Neuroscience Neuroscience ISH/FISH HALO
Multiregional single-cell dissection of tumor and immune cells reveals stable lock-and-key features in liver cancer Ma L, Heinrich S, Wang L, Keggenhoff F, Khatib S, Forgues M, Kelly M, Hewitt S, Saif A, Hernandez J, Mabry D, Kloeckner R, Greten T, Chaisaingmongkol J, Ruchirawat M, Marquardt J, Wang X 2022 Nature Communications Oncology ISH/FISH HALO
Autologous T cell therapy for MAGE-A4+ solid cancers in HLA-A*02+ patients: a phase 1 trial Hong D, Van Tine B, Biswas S, McAlpine C, Johnson M, Olszanski A, Clarke J, Araujo D, Blumenschein G, Kebriaei P, Lin Q, Tipping A, Sanderson J, Wang R, Trivedi T, Annareddy T, Bai J, Rafail S, Sun A, Fernandes L, Navenot J-M, Bushman F, Everett J, Karadeniz D, Broad R, Isabelle M, Naidoo R, Bath N, Betts G, Wolchinsky Z, Batrakou D, Van Winkle E, Elefant E, Ghobadi A, Cashen A, Grand'Maison A, McCarthy P, Fracasso P, Norry E, Williams D, Druta M, Liebner D, Odunsi K, Butler M 2023 Nature Medicine Immuno-oncology ISH/FISH, Spatial Analysis, Highplex FL HALO
Combined KRASG12C and SOS1 inhibition enhances and extends the anti-tumor response in KRASG12C-driven cancers by addressing intrinsic and acquired resistance Thatikonda V, Lu H, Jurado S, Kostyrko K, Bristow C, Bosch K, Feng N, Gao S, Gerlach D, Gmachi M, Lieb S, Jeschko A, Machado A, Marszalek E, Mahendra M, Jaeger P, Sorokin A, Strauss S, Trapani F, Kopetz S, Vellano C, Petronczki M, Kraut N, Heffernan T, Marszalek J, Pearson M, Waizenegger I, Hofmann M 2023 bioRxiv Oncology ISH/FISH, Multiplex IHC, Highplex FL, Figure Maker HALO
Prefrontal cortical protease TACE/ADAM17 is involved in neuroinflammation and stress-related eating alterations Sharafeddin F, Ghaly M, Simon T, Ontiveros-Angel P, Figueroa J 2023 bioRxiv Neuroscience ISH/FISH HALO
Long noncoding RNA LINC01594 inhibits the CELF6-mediated splicing of oncogenic CD44 variants to promote colorectal cancer metastasis. Liu B, Song A, Gui P, Wang J, Pan Y, Li C, Li S, Zhang Y, Jiang T, Xu Y, Huo F, Pei D, Song J 2023 Research Square Oncology ISH/FISH HALO
CD47-Dependent Regulation of Immune Checkpoint Gene Expression and MYCN mRNA Splicing in Murine CD8 and Jurkat T Cells Kaur S, Awad D, Finney R, Meyer T, Singh S, Cam M, Karim B, Warner A, Roberts D 2023 International Journal of Molecular Sciences Immuno-oncology ISH/FISH HALO
SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence Gioia U, Tavella S, Martinez-Orellana P, Cicio G, Colliva A, Ceccon M, Cabrini M, Henriques A, Fumagalli V, Paldino A, Presot E, Rajasekharan S, Iacomino N, Pisati F, Matti V, Sepe S, Conte M, Barozzi S, Lavagnino Z, Carletti T, Volpe M, Cavalcante P, Iannacone M, Rampazzo C, Bussani R, Tripodo C, Zacchigna S, Marcello A, di Fagagna F 2023 Nature Cell Biology Infectious Disease ISH/FISH, Highplex FL HALO
A cellular and molecular spatial atlas of dystrophic muscle Stec M, Su Q, Adler C, Zhang L, Golann D, Khan N, Panagis L, Villalta S, Ni M, Wei Y, Walls J, Murphy A, Yancopoulos G, Atwal G, Kleiner S, Halasz G, Sleeman M 2023 Proceedings of the National Academy of Sciences Myology ISH/FISH, Highplex FL HALO

Related HALO Modules

TMA (Tissue Microarray) Add-On

Module to assist in the segmentation of TMA spots for further analysis.

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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-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.

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