Before Markup

ISH Module

Try It Out

Use the HALO® ISH module and reagents from Molecular Instruments or ACD, a Bio-techne brand, to simultaneously analyze up to three nucleic acid probes on a cell-by-cell basis. This module measures chromogenic and/or silver-labelled DNA or RNA ISH probes in the nucleus and cytoplasm, enabling in-depth analysis of spot numbers and area per cell and compartment, and calculated H-scores for each probe. Analysis can be optimized by incorporating pre-trained AI-based nuclear segmentation, now included with the HALO platform, while interactive markups streamline exploring probe colocalization and combined cell phenotypes.​

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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

RNAscope™ Image Analysis Using HALO and HALO AI

Using our ISH module for brightfield and our FISH module for fluorescence, we demonstrate how to quantify ISH signal from RNAscope™ assays based on ACD Bio’s recommended scoring guidelines.

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Glomeruli Quantification and Characterization Application Note

Don’t let varied stain selections hold back your digital image analysis of kidney sections! With HALO AI you can develop a tissue classifier that accurately detects and segments glomeruli in sections across a range of stains including H&E, trichrome, PAMS, and DAB with hematoxylin.

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Indica Labs, Inc. will use the information you provide on this form to provide updates and marketing, including but not limited to, webinars, events, and software releases. We will treat your information with respect. You can unsubscribe from our emails at any time. For more information about our privacy practices please read our Privacy Policy.
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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.

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Indica Labs, Inc. will use the information you provide on this form to provide updates and marketing, including but not limited to, webinars, events, and software releases. We will treat your information with respect. You can unsubscribe from our emails at any time. For more information about our privacy practices please read our Privacy Policy.
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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.

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Indica Labs, Inc. will use the information you provide on this form to provide updates and marketing, including but not limited to, webinars, events, and software releases. We will treat your information with respect. You can unsubscribe from our emails at any time. For more information about our privacy practices please read our Privacy Policy.
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Publication Spotlight

The table below includes publications that cite the ISH Quantification module. 

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

Title Authors Year Journal Application HALO Modules Product
Lipid Source and Peroxidation Status Alter Immune Cell Recruitment in Broiler Chicken Ileum Fries-Craft KA, Meyer MM, Lindblom SC, Kerr BJ, Bobeck EA 2021 The Journal of Nutrition Immunology ISH/FISH HALO
A distinct repertoire of cancer-associated fibroblasts is enriched in cribriform prostate cancer Hesterberg AB, Rios BL, Wolf EM, Tubbs C, Wong HY, Schaffer KR, Lotan TL, Giannico GA, Gordetsky JB, Hurley PJ 2021 Journal of Pathology:Clinical Research Oncology Classifier, ISH/FISH HALO
CD8+ T cells fail to limit SIV reactivation following ART withdrawal until after viral amplification Okoye AA, Duell DD, Fukazawa Y, Varco-Merth B, Marenco A, Behrens H, Chaunzwa TM, Selseth AN, Gilbride RM, Shao J, Edlefsen PT, Geleziunas R, Pinkevych M, Davenport MP, Busman-Sahay K, Nekorchuk MD, Park H, Smedley JV, Axthelm MK, Estes JD, Hansen SG, Keele BF, Lifson JD, Picker LJ 2021 The Journal of Clinical Investigation Immunology, Infectious Disease ISH/FISH HALO, HALO AI
A first-in-human, phase 1, dose-escalation study of ABBV-176, an antibody-drug conjugate targeting the prolactin receptor, in patients with advanced solid tumors Lemech C, Woodward N, Chan N, Mortimer J, Naumovski L, Nuthalapati S, Tong B, Jiang F, Ansell P, Ratajczak CK, Sachdev J 2020 Investigational New Drugs Oncology ISH/FISH HALO
Gene expression of prostaglandin EP4 receptor in three canine carcinomas Musser ML, Viall AK, Phillips RL, Hostetter JM, Johannes CM 2020 BMC Veterinary Research Oncology ISH/FISH HALO
Cholecystokinin-1 receptor agonist induced pathological findings in the exocrine pancreas of non-human primates Nyborg NCB, Kirk RK, de Boer AS, Andersen DW, Bugge A, Wulff BS, Thorup I, Clausen TR 2020 Toxicology & Applied Pharmacology Metabolism ISH/FISH HALO
NPY mediates the rapid feeding and glucose metabolism regulatory functions of AgRP neurons Ruud LE, Pereira MMA, de Solis AJ, Fenselau H, Bruning JC 2020 Nature Communications Metabolism ISH/FISH HALO
Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 infection in the lung epithelium Schuler BA, Habermann AC, Plosa EJ, Taylor CJ, Jetter C, Kapp ME, Benjamin JT, Gullerman P, Nichols DS, Braunstein LZ, Hackett A, Koval M, Guttentag SH, Blackwell TS, Webber SA, Banovich NE, Kropski JA, Sucre JMS 2020 The Journal of Clincial Invesitgation Infectious Disease ISH/FISH HALO
The human IL-15 superagonist N-803 promotes migration of virus-specific CD8+ T and NK cells to B cell follicles but does not reverse latency in ART-suppressed, SHIV-infected macaques Webb GM, Molden J, Bushman-Sahay K, Abdulhaqq S, Wu HL, Weber WC, Bateman KB, Reed JS, Northrup M, Maier N,Tanaka S, Gao L, Davey B, Carpenter BL, Axthelm MK, Stanton JJ, Smedley J, Greene JM, Safrit JT, Estes JD, Skinner PJ, Sacha JB 2020 PLOS Pathogens Infectious Disease Cytonuclear, ISH/FISH HALO
Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake Adriaenssens AE, Biggs EK, Darwish T, Tadross J, Sukthankar T, Girish M, Polex-Wolf J, Lam BY, Zvetkova I, Pan W, Chiarugi D, Yeo GSH, Blouet C, Gribble FM, Reimann F 2019 Cell Metabolism Metabolism ISH/FISH HALO
Detection and quantification of†Parascaris†P-glycoprotein drug transporter expression with a novel mRNA hybridization technique Chelladurai JJ, Brewer MT 2019 Veterinary Parasitology Infectious Disease ISH/FISH HALO
IL-7-dependent compositional changes within the ?? T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response Chen H-C, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT, de la Roche M 2019 EMBO Reports Oncology, Immuno-oncology ISH/FISH HALO
Assessment of PD-L1 mRNA and protein expression in non-small cell lung cancer, head and neck squamous cell carcinoma and urothelial carcinoma tissue specimens using RNAScope and immunohistochemistry Duncan DJ, Scott M, Scorer P, Barker C 2019 PLOS One Oncology, Immuno-oncology ISH/FISH HALO
Expression of cholecystokinin by neurons in mouse spinal dorsal horn Guitierrez-Mecinas M, Bell AM, Shepherd F, Polgar E, Watanabe M, Furuta T, Todd AJ 2019 The Journal of Comparitive Neurology Neuroscience ISH/FISH HALO
Neurexin 3 transmembrane and soluble isoform expression and splicing haplotype are associated with neuron inflammasome and Alzheimer's disease Hishimoto A, Pletnikova O, Lang DL, Troncoso JC, Egan JM, Liu Q-R 2019 Alzheimer's Research & Therapy Neuroscience ISH/FISH HALO
Development of resistance to FAK inhibition in pancreatic cancer is linked to stromal depletion Jiang H, Liu X, Knolhoff BL, Hegde S, Lee KB, Jiang H, Fields RC, Pachter JA, Lim K-H, DeNardo DG 2019 Gut Oncology Cytonuclear, ISH/FISH HALO
Single-Cell Quantification of mRNA Expression in The Human Brain Jolly S, Lang V, Koelzer VH, Frigerio CS, Magno L, Salinas PC, Whiting P, Palomer E 2019 Scientific Reports Neuroscience ISH/FISH HALO
The Fat Mass and Obesity-Associated Protein (FTO) Regulates Locomotor Responses to Novelty via D2R Medium Spiny Neurons Ruud J, Alber J, Tokarska A, Engstrˆm Ruu L, Nolte H, Biglari N, Lippert R, Lautenschlager ƒ, Cie?lak PE, Szumiec ?, Hess ME, Brˆnneke HS, Kr¸ger M, Nissbrandt H, Korotkova T, Silberberg G, Rodriguez Parkitna J, Br¸ning J 2019 Cell Reports Neuroscience, Metabolism ISH/FISH HALO
Quantitative digital pathology reveals association of cell-specific PNPLA3 transcription with NAFLD disease activity Sandhu B, Perez Matos MC, Tran S, Zhong A, Csizmadia E, Kim M, Herman MA, Nasser I, Lai M, Jiang ZG 2019 JHEP Reports Fibrosis ISH/FISH HALO
Alpha-synuclein is a DNA binding protein that modulates DNA repair with implications for Lewy body disorders Schaser AJ, Osterberg VR, Dent SE, Stackhouse TL, Wakeham CM, Boutros SW, Weston LJ, Owen N, Weissman TA, Luna E, Raber J, Luk KC, McCullough AK, Woltjer RL, Unni VK 2019 Scientific Reports Neuroscience ISH/FISH HALO
Small Molecule IL-36? Antagonist as a Novel Therapeutic Approach for Plaque Psoriasis Todorovi? V, Su Z, Putman CB, Kakavas SJ, Salte KM, McDonald HA, Wetter JB, Paulsboe SE, Sun Q, Gerstein CE, Medina L, Sielaff B, Sadhukhan R, Stockmann H, Richardson PL, Qiu W, Argiriadi MA, Henry RF, Herold JM, Shotwell JB, McGaraughty SP, Honore P, Gopalakrishnan SM, Sun CC, Scott VE 2019 Scientific Reports Immunology, Dermatology ISH/FISH HALO
Expression of avian ?-defensin mRNA in the chicken yolk sac Zhang H, Wong EA 2019 Developmental & Comparative Immunology Immunology ISH/FISH HALO
TGF? inhibition restores a regenerative response in acute liver injury by suppressing paracrine senescence Bird TG, M¸ller M, Boulter L, Vincent DF, Ridgway RA, Elena Lopez-Guadamillas E, Lu W-Y, Jamieson T, Govaere O, Campbell AD, Ferreira-Gonzalez S, Cole AM, Hay T, Simpson KJ, Clark W, Hedley A, Clarke M, Gentaz P, Nixon C, Bryce S, Kiourtis C, Sprangers J, Nibbs RJB, Van Rooijen N, Bartholin L, McGreal SR, Apte U, Barry ST, Iredale JP, Clarke AR, Serrano M, Roskams TA, Sansom OJ, Forbes SJ 2018 Science Translational Medicine Metabolism ISH/FISH HALO
Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation Brandt C, Nolte H, Henschke S, Ruud LE, Awazawa M, Morgan DA, Gabel P, Sprenger H-G, Hess ME, G¸nther S, Langer T, Rahmouni K, Fenselau H, Kr¸ger M, Br¸ning JC 2018 Cell Neuroscience, Metabolism ISH/FISH HALO
Gene Signature of Proliferating Human Pancreatic ?-Cells Dominguez Gutierrez G, Xin Y, Okamoto H, Kim J, Lee A-H, Ni M, Adler C, Yancopoulos GD, Murphy AJ, Gromada J 2018 Endocrionology Metabolism ISH/FISH HALO
A phase II study of the dual mTOR inhibitor MLN0128 in patients with metastatic castration resistant prostate cancer Graham L, Banda K, Torres A, Carver BS, Chen Y, Pisano K, Shelkey G, Curley T, Scher HI, Lotan TL, Hsieh AC, Rathkopf DE 2018 Investigational New Drugs Oncology ISH/FISH HALO
Ultrasensitive automated RNA in situ hybridization for kappa and lambda light chain mRNA detects B-cell clonality in tissue biopsies with performance comparable or superior to flow cytometry Guo L, Wang Z, Anderson CA, Doolittle E, Kernag S, Cotta CV, Ondrejka SL, Ma X-J, Cook JR 2018 Modern Pathology Other Classifier, ISH/FISH HALO
Mutant myocilin impacts sarcomere ultrastructure in mouse gastrocnemius muscle Lynch JM, Dolman AJ, Guo C, Dolan K, Xiang C, Reda S, Li B, Prasanna G 2018 PLOS One Gastroenterology, Myology ISH/FISH HALO
Breast and pancreatic cancer interrupt IRF8-dependent dendritic cell development to overcome immune surveillance Meyer MA, Baer JM, Knolhoff BL, Nywening TM, Panni RZ, Su X, Weilbaecher KN, Hawkins WG, Ma C, Fields RC, Linehan DC, Challen GA, Faccio R, Aft RL, DeNardo DG 2018 Nature Communications Oncology, Immuno-oncology ISH/FISH HALO
APNG as a prognostic marker in patients with glioblastoma Fosmark S, Hellwege S, Dahlrot RH, Jensen KL, Derand H, Lohse J, S¯rensen MD, Hansen S, Kristensen BW 2017 PLOS One Oncology ISH/FISH HALO
A randomized, open-label study of the efficacy and safety of AZD4547 monotherapy versus paclitaxel for the treatment of advanced gastric adenocarcinoma with†FGFR2†polysomy or gene amplification Van Cutsem E, Bang Y-J, Mansoor W, Petty RD, Chao Y, Cunningham D, Ferry DR, N. R. Smith NR, Frewer P, Ratnayake J, Stockman PK, Kilgour E, and Landers D 2017 Annals of Oncology Oncology Classifier, ISH/FISH HALO
Fully automated RNAscope in situ hybridization assays for formalin?fixed paraffin?embedded cells and tissues Anderson CM, Zhang B, Miller M, Butko E, Wu X, Laver T, Kernag C, Kim J, Luo Y, Lamparski H 2016 Journal of Cellular Biochemistry Oncology, Gastroenterology, Infectious Disease ISH/FISH HALO
Variability in Platelet-Derived Growth Factor Receptor Alpha Antibody Specificity May Impact Clinical Utility of Immunohistochemistry Assays Holzer TR, Reising LO, Credille KM, Schade AE, Oakley 2016 Journal of Histochemistry & Cytochemistry Oncology Cytonuclear, ISH/FISH HALO
Differential Cytokine Gene Expression in Granulomas from Lungs and Lymph Nodes of Cattle Experimentally Infected with Aerosolized Mycobacterium bovis Palmer MV, Thacker TC, Waters WR 2016 PLOS One Infectious Disease ISH/FISH HALO
RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes Xin Y, Kim J, Okamoto H, Ni M, Wei Y, Adler C, Murphy AJ, Yancopoulos GD, Lin C, Gromada J 2016 Cell Metabolism Metabolism ISH/FISH HALO
G-protein-independent coupling of MC4R to Kir7. 1 in hypothalamic neurons Ghamari-Langroudi M, Digby GJ, Sebag JA, Millhauser GL, Palomino R, Matthews R, Gillyard T, Panaro BL, Tough IR, Cox HM, Denton JS, Cone RD 2015 Nature Metabolism ISH/FISH HALO
Activation of the renal GLP?1R leads to expression of Ren1 in the renal vascular tree Bj¯rnholm KD, Ougaard ME, Skovsted GF, Knudsen LB, Pyke C 2021 Endocrinology, Diabetes, & Metabolism Metabolism ISH/FISH HALO
A Method to Pre-Screen Rat Mammary Gland Whole-Mounts Prior To RNAscope Duderstadt EL, Sanders MA, Samuelson DJ 2021 Journal of Mammary Gland Biology and Neoplasia ISH/FISH HALO
Age-associated expression of p21and p53 during human wound healing Chia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L 2021 Aging Cell Dermatology Area Quantification, ISH/FISH, Multiplex IHC HALO
Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cells Newman AC, Falcone M, Uribe AH, Zhang T, Athineos D, Pietzke M, Vazquez A, Blyth K, Maddocks ODK 2021 Molecular Cell Immuno-oncology Classifier, ISH/FISH HALO
VGLUT2 is a determinant of dopamine neuron resilience in a rotenone model of dopamine neurodegeneration Buck SA, De Miranda BR, Logan RW, Fish KN, Greenamyre JT, Freyberg Z 2021 The Journal of Neuroscience Neuroscience ISH/FISH HALO
Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaques Bochart RM, Busman-Sahay K, Bondoc S, Morrow DW, Ortiz AM, Fennessey CM, Fischer MB, Shiel O, Swanson T, Shriver-Munsch CM, Crang HB, Armantrout KM, Barber-Axthelm AM, Langner C, Moats CR, Labriola CS, MacAllister R, Axthelm MK, Brenchley JM, Keele BF, Estes JD, Hansen SG, Smedley JV 2021 PLOS Pathogens Infectious Disease ISH/FISH, Multiplex IHC HALO
Mucosal IFNγ production and potential role in protection in Escherichia coli O157:H7 vaccinated and challenged cattle Schaut RG, Palmer MV, Boggiatto PM, Kudva IT, Loving CL, Sharma VK 2021 Scientific Reports Immunology ISH/FISH HALO
Functionally distinct POMC-expressing neuron subpopulations in hypothalamus revealed by intersectional targeting Biglari N, Gaziano I, Schumacher J, Radermacher J, Paeger L, Klemm P, Chen W, Corneliussen S, Wunderlich CM, Sue M, Vollmar S, Klˆckener T, Sotelo-Hitschfeld T, Abbasloo A, Edenhofer F, Reimann F, Gribble FM, Fenselau H, Kloppenburg P, Wunderlich FT, Br¸ning JC 2021 Nature Neuroscience Neuroscience ISH/FISH HALO
Oncogenic BRAF, unrestrained by TGF?-receptor signalling, drives right-sided colonic tumorigenesis Leach J, Vlahov N, Tsantoulis P, et al 2021 Nature Communications Oncology ISH/FISH, Highplex FL HALO
Lawsonia intracellularis infected enterocytes lack sucrase-isomaltase which contributes to†reduced pig digestive capacity Helm E, Burrough E, Leite, F, Gabler, N 2021 Veterinary Research Other ISH/FISH HALO
Mechanism of Nucleic Acid Sensing in Retinal Pigment Epithelium (RPE): RIG-I Mediates Type I Interferon Response in Human RPE Schustak J, Twarog M, Wu X, Huang Q, Bao Y 2021 Journal of Immunology Research Area Quantification, ISH/FISH HALO
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer Najumudeen AK, Ceteci F, Fey SK, Hamm G, Steven RT, Hall H, Nikula CJ, Dexter A, Murta T, Race AM, Sumpton D, Vlahov N, Gay DM, Knight JRP, Jackstadt R, Leach JDG, Ridgway RA, Johnson ER, Nixon C, Hedley A, Gilroy K, Clark W, Malla SB, Dunne PD, Rodriguez-Blanco G, Critchlow SE, Mrowinska A, Malviya G, Solovyev D, Brown G, Lewis DY, Mackay GM, Strathdee D, Tardito S, Gottlieb E, CRUK Rosetta Grand Challenge Consortium, Takats Z, Barry ST, Goodwin RJA, Bunch J, Bushell M, Campbell AD, Sansom OJ 2021 Nature Genetics Oncology ISH/FISH HALO
Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8+ cells McBrien JB, Mavigner M, Li LF, Smith SA, White E, Tharp GK, Walum H, Busman-Suhay K, Aguilera-Sandoval CR, Thayer WO, Spagnuolo RA, Kovarova M, Wahl A, Cervasi B, Margolis DM, Vanderford TH, Carnathan DG, Paiardini M, Lifson JD, Lee JH, Safrit JT, Bosinger SE, Estes JD, Derdeyn CA, Garcia JV, Kulpa DA, Chahroudi A, Silvestri G 2020 Nature Other ISH/FISH HALO
CTLA-4 and PD-1 dual blockade induces SIV reactivation without control of rebound after antiretroviral therapy interruption Harper J, Gordon S, Chan CN, Wang H, Lindemuth E, Galardi C, Falcinelli SD, Raines SLM, Read JL, Nguyen K, McGary CS, Nekorchuk M, Busman-Sahay K, Schawalder J, King C, Pino M, Micci L, Cervasi B, Jean S, Sanderson A, Johns B, Koblansky AA, Amrine-Madsen H, Lifson J, Margolis DM, Silvestri G, Bar KJ, Favre D, Estes JD, Paiardini 2020 Nature Medicine Immunology, Infectious Disease Cytonuclear, ISH/FISH HALO
HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cells Wang Y, Lifschitz L, Gellatly K, Vinton CL, Busman-Sahay K, McCauley S, Vangala P, Kim K, Derr, Jaiswall S, Kucukural A, McDonel P, Hunt PW, Greenough T, Houghton J, Somsouk M, Estes JD, Brenchley JM, Garber M, Deeks SG, Luban J 2020 Nature Immunology Immunology, Infectious Disease Area Quantification, Cytonuclear, ISH/FISH HALO
Glucagon Receptor Inhibition Reduces Hyperammonemia and Lethality in Male Mice with Urea Cycle Disorder Cavino K, Sung B, Su Q, Na E, Kim J, Cheng X, Gromada J, Okamoto H 2020 Endocrinology Metabolism ISH/FISH, Multiplex IHC HALO
Chronic stress differentially alters mRNA expression of opioid peptides and receptors in the dorsal hippocampus of female and male rats Johnson MA, Contoreggi NH, Kogan JF, Bryson M, Rubin BR, Gray JD, Kreek MJ, McEwen BS, Milner TA 2021 The Journal of Comparative Neurology Neruoscience ISH/FISH HALO
Monocyte and macrophage derived myofibroblasts: Is it fate? A review of the current evidence Vierhout M, Ayoub A, Naiel S, Yazdanshenas P, Revill S, Reihani A, Dvorkin-Gheva A, Shi W, Ask K 2021 Wound Repair and Regeneration Review ISH/FISH HALO
Alteration of Colonic Mucin Composition and Cytokine Expression in Acute Swine Dysentery Lin S J-H, Arruda B, Burrough E 2021 Veterinary Pathology Immunology Area Quantification, ISH/FISH HALO
Orexin receptors 1 and 2 in serotonergic neurons differentially regulate peripheral glucose metabolism in obesity Xiao X Yeghiazaryan G, Hess S, Klemm P, Sieben A, Kleinridders A, Morgan D, Wunderlich F. Rahmouni K. Kong D, Scammell T, Lowell B, Kloppenburg P, Br¸ning J, Hausen A. 2021 Nature Communications Metabolism ISH/FISH HALO
Three subtypes of lung cancer fibroblasts definedistinct therapeutic paradigms Hu H, Peotrowska Z, Hare P, Chen H, Mulvey H, Mayfield A, Noeen S, Kattermann K, Greenberg M, Williams A, Riley A, Wilson J, Mao Y, Huang R, Banwait M, Ho J, Crowther G, Hariri L, Sequist L, Benes C, Niederst M, Engelman J 2021 Cancer Cell Oncology Cytonuclear, ISH/FISH HALO
Functional heterogeneity of POMC neurons relies on mTORC1 signaling Saucisse N, Mazier W, Simon V, Binder E, Catania C, Bellocchio L, Romanov R, Leon S, Matias I, Zizzari P, Quarta C, Cannich A, Meece K, Gonzales D, Clark S, Becker J, Yeo G, Fioramonti X, Merkle F, Wardlaw S, Harkany T, Massa F, Marsicano G, Cota D 2021 Cell Reports Neuroscience ISH/FISH HALO
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
Transcriptomic analysis links diverse hypothalamic cell types to fibroblast growth factor 1-induced sustained diabetes remission Bentsen MA, Rausch DM, Mirzadeh Z, Muta K, Scarlett JM, Brown JM, Herranz-Perez V, Baquero AF, Thompson J, Alonge KM, Faber CL, Kaiyala KJ, Bennett C, Pyke C, Ratner C, Egerod KL, Holst B, Meek TH, Kutlu B, Zhang Y, Sparso T, Grove KL, Morton GJ, Kornum BR, Garcia-Verdugo J-M, Secher A, Jorgensen R, Schwartz MW, Pers TH 2020 Nature Communications Metabolism ISH/FISH HALO
PPAR-gamma induced AKT3 expression increases levels of mitochondrial biogenesis driving prostate cancer Galbraith L, Mui E, Nixon C, Hedley A, Strachan D, MacKay G, Sumpton D, Sansom O, Leung H, Ahmad I 2021 Oncogene Oncology ISH/FISH HALO
Cross-Platform Comparison of Computer-assisted Image Analysis Quantification of In Situ mRNA Hybridization in Investigative Pathology Holzer TR, Hanson JC, Wray EM, Bailey JA, Kennedy KR, Finnegan PR, Nasir A, Credille KM 2019 Applied Immunohistochemistry & Molecular Morpholgy Other ISH/FISH HALO
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
Age-associated expression of p21 and p53 during human wound healing Chia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L 2021 Aging Cell Dermatology Area Quantification, ISH/FISH, Multiplex IHC 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
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
Transcriptional and functional divergence in lateral hypothalamic glutamate neurons projecting to the lateral habenula and ventral tegmental area Rossi M, Basiri M, Liu Y, Hashikawa Y, Hashikawa K, Fenno L, Kim Y, Ramakrishnan C, Deisseroth K, Stuber G 2021 Neuron Neuroscience ISH/FISH HALO
Genetic suppression of the dopamine D3 receptor in striatal D1 cells reduces the development of L-DOPA-induced dyskinesia Lanza K, Centner A, Coyle M, Del Priore I, Manfredsson F, Bishop C 2021 Experimental Neurology Neuroscience ISH/FISH HALO
An endogenous opioid circuit determines state-dependent reward consumption Castro D, Oswell C, Zhang E, Pedersen C, Piantadosi S, Rossi M, Hunker A, Guglin A, Moron J, Zweifel L, Stuber G, Bruchas M 2021 Nature Neuroscience ISH/FISH HALO
Sex differences in the rodent hippocampal opioid system following stress and oxycodone associated learning processes Chalangal J, Mazid S, Windisch K, Milner T 2021 Pharmacology Biochemistry and Behavior Review ISH/FISH 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
Engineering Cancer Antigen-Specific T Cells to Overcome the Immunosuppressive Effects of TGF-_ Silk J, Abbott R Adams K, Bennett A, Brett S, Cornforth T, Crossland K, Figueroa D, Jing J, O'Conner C, Pachnio A, Patasic L, Peredo C, Quattrini A, Quinn L, Rust A, Saini M, Sanderson J, Steiner D, Tavano B, Viswanathan P, Wiedermann G, Wong R, Jakobsen B, Britten C, Gerry A, Brewer J 2021 The Journal of Immunology Immuno-oncology, other ISH/FISH HALO
A single-cell atlas of mouse lung development Negretti N, Plosa E, Benjamin J, Schuler B, Habermann A, Jetter C, Gulleman P, Bunn C, Hackett A, Ransom M, Taylor C, Nichols D, Matlock B, Guttentag S, Blackwell T, Banovich N, Kropski J, Sucre J 2021 Development Other ISH/FISH 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
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
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
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
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
IL17A mRNA staining distinguishes palmoplantar psoriasis from hyperkeratotic palmoplantar eczema in diagnostic skin biopsies Chen J, Murphy M, Singh K, Wang A, Chow R, Kim S, Cohen J, Ko C, Damsky W 2023 JID Innovations Dermatology ISH HALO
Oncogenic KrasG12D specific non-covalent inhibitor reprograms tumor microenvironment to prevent and reverse early pre-neoplastic pancreatic lesions and in combination with immunotherapy regresses advanced PDAC in a CD8+ T cells dependent manner Mahadevan K, McAndrews K, LeBlue V, Yang S, Lyu H, Li B, Sockwell A, Kirtley M, Morse S, Diaz B, Kim M, Feng N, Lopez A, Guerrero P, Sugimoto H, Arian K, Ying H, Barekatain Y, Kelly P, Maitra A, Heffernan T, Kalluri R 2023 bioRxiv Oncology FISH, Highplex FL HALO
In-depth virological and immunological characterization of HIV-1 cure after CCR5Δ32/Δ32 allogeneic hematopoietic stem cell transplantation Jensen B, Knops E, Cords L, Lubke N, Salgado M, Busman-Sahay K, Estes J, Huyveneers L, Perdomo-Celis F, Wittner M, Galvez C, Mummert C, Passaes C, Eberhard J, Munk C, Hauber I, Hauber J, Heger E, De Clercq J, Vandekerckhove L, Bergmann S, Dunay G, Klein F, Haussinger D, Fischer J, Nachtkamp K, Timm J, Kaiser R, Harrer T, Luedde T, Nijhuis M, Saez-Cirion A, zur Wiesch J, Wensing A, Martinez-Picado J, Kobbe G 2023 Nature Medicine Infectious Disease ISH, Figure Maker 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
Myeloid-specific deletion of activating transcription factor 6 alpha increases CD11b+ macrophage subpopulations and aggravates lung fibrosis Mekhael O, Revill S, Hayat A, Cass S, MacDonald K, Vierhout M, Ayoub A, Reihani A, Padwal M, Imani J, Ayaub E, Yousof T, Dvorkin-Gheva A, Rullo A, Hirota J, Richards C, Bridgewater D, Stämpfli M, Hambly N, Naqvi A, Kolb M, Ask K 2023 Immunology and Cell Biology Immunology, Fibrosis Classifier, Area Quantification, FISH, Multiplex IHC HALO
Metabolic profiling stratifies colorectal cancer and reveals adenosylhomocysteinase as a therapeutic target Voorde J, Najumudeen A, Steven R, Nikula C, Dexter A, Zeiger L, Elia E, Nasif A, Conzalez-Fernandez A, Murta T, Gillespie M, Ford C, Lannagan T, Vlahov N, Ridgeway R, Nixon C, Gilroy K, Gay D, Burton A, Yan B, Sellers K, Wu V, Xiang Y, Shokry E, Clark W, Li V, Barry S, Goodwin R, Takats Z, Maddocks O, Sumpton D, Yuneva M, Campbell A, Bunch J, Sansom O 2023 bioRxiv Oncology ISH 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
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
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
Pseudoknot-targeting Cas13b combats SARS-CoV-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
Chronic immune activation and gut barrier dysfunction is associated with neuroinflammation in ART-suppressed SIV+ rhesus macaques Byrnes S, Busman-Sahay K, Angelovich T, Younger S, Taylor-Brill S, Nekorchuk M, Bondoc S, Dannay R, Terry M, Cochrane C, Jenkins T, Roche M, Deleage C, Bosinger S, Paiardini M, Brew B, Estes J, Churchill M 2023 PLOS Pathogens Infectious Disease Area Quantification, Object Colocalization, ISH, Highplex FL HALO
Dedifferentiation maintains melanocyte stem cells in a dynamic niche Sun Q, Lee W, Hu H, Ogawa T, De Leon S, Katehis I, Lim C, Takeo M, Cammer M, Taketo M, Gay D, Millar S, Ito M 2023 Nature Other FISH Nature
Adrenal cortex size and homeostasis are regulated by gonadal hormones via androgen receptor/β-catenin signaling crosstalk Lyraki R, Grabek A, Tison A, Weerasinghe-Arachchige L, Peitzsch M, Bechman N, Youssef S, de Bruin A, Bakker E, Claessens F, Chaboissier M, Schedl A 2023 Disease Models & Mechanisms Other FISH, Highplex FL HALO
Neural mechanism of acute stress regulation by trace aminergic signalling in the lateral habenula in male mice Yang S, Yang E, Lee J, Kim J, Yoo H, Park H, Jung J, Lee D, Chun S, Jo Y, Pyeon G, Park J, Lee H, Kim H 2023 Nature Communications Neuroscience FISH 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
D-serine availability modulates prefrontal cortex inhibitory interneuron development and circuit maturation Folorunso O, Brown S, Baruah J, Harvey T, Jami S, Radzishevsky I, Wolosker H, McNally J, Gray J, Vasudevan A, Balu D 2023 Scientific Reports Neuroscience ISH HALO
Kv7/KCNQ potassium channels in cortical hyperexcitability and juvenile seizure-related death in Ank2-mutant mice Oh H, Lee S, Oh Y, Kim S, Kim Y, Yang Y, Choi W, Yoo Y, Cho H, Lee S, Yang E, Koh W, Won W, Kim R, Lee C, Kim H, Kang H, Kim J, Ku T, Paik S, Kim E 2023 Nature Communications Neuroscience FISH 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
Localization of unlabelled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imaging Spencer-Dene B, Mukherjee P, Alex A, Bera K, Tseng W, Shi J, Chaney E, Spillman Jr. D, Marjanovic B, Miranda E, Boppart S, Hood S 2023 RNA Other ISH HALO, HALO AI
Long-Term Dysfunction of Taste Papillae in SARS-CoV-2 Yao Q, Doyle M, Liu Q, Appleton A, O'Connell J, Weng N, Egan J 2023 NEJM Evidence Infectious Disease FISH HALO
LINC01638 Sustains Human Mesenchymal Stem Cell Self-Renewal and Competency for Osteogenic Cell Fate Gordon J, Tye C, Banerjee B, Ghule P, Wijnen A, Kabala F, Page N, Falcone M, Stein J, Stein G, Lian J 2023 Research Square Other Object Colocalization, FISH 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
ABCC2 brush-border expression predicts outcome in papillary renal cell carcinoma: a multi-institutional study of 254 cases Castillo VF, Masoomian M, Trpkov K, Downes M, Brimo F, van der Kwast T, Yousef GM, Zakhary A, Rotondo F, Saad G, Nguyen V, Kidanewold W, Streutker C, Rowsell C, Hamdani M, Saleeb RM 2023 Histopathology Oncology ISH HALO
Single-cell analysis of the miRNA activities in tuberculous meningitis (TBM) model mice injected with the BCG vaccine Zhang X, Pan L, Zhang P, Wang L, Shen Y, Xu P, Ren Y, Huang W, Liu P, Wu Q, Li F 2023 International Immunopharmacology Infectious Disease FISH HALO
Osteoprogenitor recruitment and differentiation during intracortical bone remodeling of adolescent humans Christiansen PvD, Andreasen CM, El-Masri BM, Laursen KS, Delaisse JM, Andersen TL 2023 Bone Other FISH HALO, HALO AI
Characterization of expression and prognostic implications of transforming growth factor beta, programmed death-ligand 1, and T regulatory cells in canine histiocytic sarcoma Murphy J, Shiomitsu K, Milner R, Lejeune A, Ossiboff R, Gell J, Axiak-Bechtel S 2023 Veterinary Immunology and Immunopathology Oncology ISH HALO
Baseline skin cytokine profiles determined by RNA in situ hybridization correlate with response to dupilumab in patients with eczematous dermatitis Singh K, Valido K, Swallow M, Okifo K, Wang A, Cohen J, Damsky W 2023 Journal of the American Academy of Dermatology Dermatology ISH HALO
FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells Danopoulos S, Belgacemi R, Hein R, Miller A, Deutsch G, Glass I, Spence J, Al Alam D 2023 American Journal of Physiology - Lung Cellular and Molecular Physiology Other FISH HALO
A Spatial Atlas of Wnt Receptors in Adult Mouse Liver Gayden J, Hu S, Joseph P, Delgado E, Liu S, Bell A, Puig S, Monga S, Freyberg Z 2023 The American Journal of Pathology Gastroenterology FISH HALO
Vascular-Parenchymal Crosstalk Promotes Lung Fibrosis Through BMPR2 Signaling Yanagihara T, Tsubouchi K, Zhou Q, Chong M, Otsubo K, Isshiki T, Schupp J, Sato S, Scallan C, Upagupta C, Revill S, Ayoub A, Chong S, Dvorkin-Gheva A, Kaminski N, Tikkanen J, Keshavjee S, Pare G, Guignabert C, Ask K, Kolb M 2023 American Journal of Respiratory and Critical Care Medicine Fibrosis Area Quantification, ISH, TMA HALO
Intrinsic BMP inhibitor Gremlin regulates alveolar epithelial type II cell proliferation and differentiation Yanagihara T, Zhou Q, Tsubouchi K, Revill S, Ayoub A, Gholiof M, Chong S, Dvorkin-Gheva A, Ask K, Shi W, Kolb M 2023 Biochemical and Biophysical Research Communications Other ISH, TMA HALO
Characterization of expression and prognostic implications of GD2 and GD3 synthase in canine histiocytic sarcoma Murphy J, Axiak-Bechtel S, Milner R, Lejeune A, Ossiboff R, Castellanos Gell J, Shiomitsu K 2023 Veterinary Immunology and Immunopathology Oncology ISH HALO
Genetically- and spatially-defined basolateral amygdala neurons control food consumption and social interaction Lim H, Zhang Y, Peters C, Straub T, Mayer JL, Klein R 2023 bioRxiv Neuroscience FISH HALO
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
CRISPR–Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames Zheng C, Wei Y, Zhang P, Lin K, He D, Teng H, Manyam G, Zhang Z, Liu W, Lee H R L, Tang X, He W, Islam N, Jain A, Chiu Y, Cao S, Diao Y, Meyer-Gauen S, Höök M, Malovannaya A, Li W, Hu M, Wang W, Xu H, Kopetz S, Chen Y 2023 Nature Structural & Molecular Biology Oncology ISH 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
mRNA Vaccine Trafficking and Resulting Protein Expression After Intramuscular Administration Hassett KJ, Rajilic IL, Bahl K, White R, Cowens K, Jacquinet E, Burke KE 2023 Molecular Therapy: Nucleic Acid Other ISH, Multiplex IHC HALO
Induction of double-strand breaks with the non-steroidal androgen receptor ligand flutamide in patients on androgen suppression: a study protocol for a randomized, double-blind prospective trial Lee E, Coulter J, Mishra A, Caramella-Pereira F, Demarzo A, Rudek M, Hu C, Han M, DeWeese TL, Yegnasubramanian S, Song DY 2023 Trials Oncology Object Colocalization, ISH HALO
Detection of IL12/23p40 via PET Visualizes Inflammatory Bowel Disease Rezazadeh F, Ramos N, Saliganan A, Al-Hallak N, Chen K, Mohamad B, Wiesend W, Viola N 2023 Journal of Nuclear Medicine Immunology ISH HALO
Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects  Landa I, Thornton C, Xu B, Haase J, Krishnamoorthy G, Hao J, Knauf J, Herbert Z, Martinez P, Blasco M, Ghossein R, Fagin J 2023 Molecular Cancer Research Oncology FISH HALO
Spatial Transcriptomics Reveals Distinct Tissue Niches Linked with Steroid Responsiveness in Acute Gastrointestinal GVHD Patel BK, Raabe MJ, Lang ER, Song Y, Lu C, Deshpande V, Nieman LT, Aryee MJ, Chen YB, Ting DT, DeFilipp Z 2023 Blood Immunology ISH HALO
Ventral pallidum neurons projecting to the ventral tegmental area reinforce but do not invigorate reward-seeking behavior Palmer D, Cayton CA, Scott A, Lin I, Newell B, Paulson A, Weberg M, Richard JM 2024 Cell Reports Neuroscience FISH HALO
Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis Mennillo E, Kim Y, Lee G, Rusu I, Patel R K, Dorman L C, Flynn E, Li S, Bain J L, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein M L, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho S, Beck K, El-Nachef N, Lewin S, Selvig D R, Terdiman J P, Mahadevan U, Oh D Y, Fragiadakis G K, Pisco A, Combes A J, Kattah M G 2024 Nature Communications Immunology ISH, Spatial Analysis, Highplex FL, TMA HALO, HALO AI
Multi-omics and imaging mass cytometry characterization of human kidneys to identify pathways and phenotypes associated with impaired kidney function. Asowata E O, Romoli S, Sargeant R, Tan J Y, Hoffmann S, Huang M M, Mahbubani K T, Krause F N, Jachimowicz D, Agren R, Koulman A, Jenkins B, Musial B, Griffin J L, Soderberg M, Ling S, Hansen P B L, Saeb-Parsy K, Woollard K J 2024 Kidney International Other ISH, Spatial Analysis, Highplex FL HALO, HALO AI
N6-methyladenosine-modified circSLCO1B3 promotes intrahepatic cholangiocarcinoma progression via regulating HOXC8 and PD-L1 Li J, Xu X, Xu K, Zhou X, Wu K, Yao Y, Liu Z, Chen C, Wang L, Sun Z, Jiao D, Han X 2024 Journal of Experimental & Clinical Cancer Research Oncology Area Quantification, FISH, Highplex, TMA HALO
A First-in-Human Phase 1 Study of a Tumor-Directed RNA-Interference Drug against HIF2a in Patients with Advanced Clear Cell Renal Cell Carcinoma Brugarolas J, Obara G, Beckermann K E, Rini B, Lam E T, Hamilton J, Schluep T, Yi M, Wong S, Mao Z L, Gamelin E, Tannir N M 2024 Clinical Cancer Research Oncology ISH 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 2024 Journal of Pathology Oncology Spatial Analysis, FISH-IF HALO
Spatial distribution of Mycobacterium tuberculosis mRNA and secreted antigens in acid-fast negative human antemortem and resected tissue Nargan K, Glasgow J, Nadeem S, Naidoo T, Wells G, Hunter R, Hutton A, Lumamba K, Msimang M, Benson P, Steyn A 2024 EBioMedicine Infectious Disease Area Quantification, ISH HALO
Spatial multi-omics of human skin reveals KRAS and inflammatory responses to spaceflight Park J, Overbey E, Narayanan S A, Kim J, Tierney B T, Damle N, Najjar D, Ryon K A, Proszynski J, Kleinman A, Hirschberg J W, MacKay M, Afshin E E, Granstein R, Gurvitch J, Hudson B M, Rininger A, Mullane S, Church S E, Meydan C, Church G, Beheshti A, Mateus J, Mason C E 2024 Nature Communications Dermatology ISH HALO
Adjuvant COX inhibition augments STING signaling and cytolytic T cell infiltration in irradiated 4T1 tumors Ridnour L, Cheng R, Kedei N, Somasundaram V, Bhattacharyya D, Basudhar D, Wink A, Walke A, Kim C, Heinz W, Edmondson E, Butcher D, Warner A, Dorsey T, Pore M, Kinders R, Lipkowitz S, Bryant R, Rittscher J, Wong S, Hewitt S, Chang J, Shalaby A, Callagy G, Glynn S, Ambs S, Anderson S, McVicar D, Lockett S, Wink D 2024 JCI Insight Immuno-oncology Classifier, FISH, Spatial Analysis, Highplex FL HALO
Development of NR0B2 as a therapeutic target for the re-education of tumor associated myeloid cells Vidana Gamage H E, Albright S T, Smith A J, Farmer R, Shahoei S H, Wang Y, Fink E C, Jacquin E, Weisser E, Bautista R O, Henn M A, Schane C P, Nelczyk A T, Ma L, Das Gupta A, Bendre S V, Nguyen T, Tiwari S, Krawczynska N, He S, Nelson E R 2024 Cancer Letters Oncology ISH, Multiplex IHC HALO
Co-targeting SOS1 enhances the antitumor effects of KRASG12C inhibitors by addressing intrinsic and acquired resistance Thatikonda V, Lyu H, Jurado S, Kostyrko K, Bristow C A, Albrecht C, Alpar D, Arnhof H, Bergner O, Bosch K, Feng N, Gao S, Gerlach D, Gmachl M, Hinkel M, Lieb S, Jeschko A, Machado A A, Madensky T, Marszalek E D, Mahendra M, Melo-Zainzinger G, Molkentine J M, Jaeger P A, Peng D H, Schenk R L, Sorokin A, Strauss S, Trapani F, Kopetz S, Vellano C P, Petronczki M, Kraut N, Heffernan T P, Marszalek J R, Pearson M, Waizenegger I C, Hofmann M H 2024 Nature Cancer Oncology FISH, Highplex FL HALO
Metabolic imaging across scales reveals distinct prostate cancer phenotypes Sushentsev N, Hamm G, Flint L, Birtles D, Zakirov A, Richings J, Ling S, Tan J Y, McLean M A, Ayyappan V, Menih I H, Brodie C, Miller J L, Mills I G, Gnanapragasam V J, Warren A Y, Barry S T, Goodwin R J A, Barrett T, Gallagher F A 2024 Nature Communications Oncology Area Quantification, FISH, Membrane, Multiplex IHC HALO, HALO AI
Genetically- and spatially-defined basolateral amygdala neurons control food consumption and social interaction Lim H, Zhang Y, Peters C, Straub T, Luise Mayer J, Klein R 2024 Nature Communications Neuroscience FISH HALO
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
Non-human primate model of long-COVID identifies immune associates of hyperglycemia Palmer C S, Perdios C, Abdel-Mohsen M, Mudd J, Datta P K, Maness N J, Lehmicke G, Golden N, Hellmers L, Coyne C, Green K M, Midkiff C, Williams K, Tiburcio R, Fahlberg M, Boykin K, Kenway C, Russell-Lodrigue K, Birnbaum A, Bohm R, Blair R, Dufour J P, Fischer T, Saied A A, Rappaport J 2024 Nature Communications Infectious Disease ISH, Highplex FL HALO
Mapping RANKL- and OPG-expressing cells in bone tissue: the bone surface cells as activators of osteoclastogenesis and promoters of the denosumab rebound effect El-Masri B M, Andreasen C M, Laursen K S, Kofod V B, Dahl X G, Nielsen M H, Thomsen J S, Brüel A, Sørensen M S, Hansen L J, Kim A S, Taylor V E, Massarotti C, McDonald M M, You X, Charles J F, Delaisse J-M, Andersen T L 2024 Bone Research Myology ISH, Spatial Analysis HALO, HALO AI

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-IHC

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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FISH

Simultaneously analyze an unlimited number of fluorescent nucleic acid 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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