Before Markup

FISH Module

Use the HALO® FISH module and reagents from Molecular Instruments or ACD, a Bio-techne brand, to simultaneously analyze an unlimited number of nucleic acid probes on a cell-by-cell basis. This module measures fluorescent 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. Optimize your analysis by incorporating pre-trained AI-based nuclear segmentation, now included with the HALO platform, and leverage interactive markups to explore probe 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

HiPlex RNAscope™ Application Note

Using our FISH module we demonstrate how to perform 12-plex RNAscope image analysis using ACD’s HiPlexv2 assay.

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.

Spatial Multiplex Profiling of Immune Markers with the RNAscope Hiplex v2 Assay

Download this poster to learn about combining ACD’s HiPlex v2 in situ hybridization assay with HALO image analysis.

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 and ISH modules. 

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

TitleAuthorsYearJournalApplicationHALO ModulesProduct
Lipid Source and Peroxidation Status Alter Immune Cell Recruitment in Broiler Chicken Ileum Fries-Craft KA, Meyer MM, Lindblom SC, Kerr BJ, Bobeck EA2021The Journal of NutritionImmunologyISH/FISHHALO
A distinct repertoire of cancer-associated fibroblasts is enriched in cribriform prostate cancerHesterberg AB, Rios BL, Wolf EM, Tubbs C, Wong HY, Schaffer KR, Lotan TL, Giannico GA, Gordetsky JB, Hurley PJ2021Journal of Pathology:Clinical ResearchOncologyClassifier, ISH/FISHHALO
CD8+ T cells fail to limit SIV reactivation following ART withdrawal until after viral amplificationOkoye 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 LJ2021The Journal of Clinical InvestigationImmunology, Infectious DiseaseISH/FISHHALO, 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 tumorsLemech C, Woodward N, Chan N, Mortimer J, Naumovski L, Nuthalapati S, Tong B, Jiang F, Ansell P, Ratajczak CK, Sachdev J2020Investigational New DrugsOncologyISH/FISHHALO
Gene expression of prostaglandin EP4 receptor in three canine carcinomasMusser ML, Viall AK, Phillips RL, Hostetter JM, Johannes CM2020BMC Veterinary ResearchOncologyISH/FISHHALO
Cholecystokinin-1 receptor agonist induced pathological findings in the exocrine pancreas of non-human primatesNyborg NCB, Kirk RK, de Boer AS, Andersen DW, Bugge A, Wulff BS, Thorup I, Clausen TR2020Toxicology & Applied PharmacologyMetabolismISH/FISHHALO
NPY mediates the rapid feeding and glucose metabolism regulatory functions of AgRP neuronsRuud LE, Pereira MMA, de Solis AJ, Fenselau H, Bruning JC2020Nature CommunicationsMetabolismISH/FISHHALO
Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 infection in the lung epitheliumSchuler 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 JMS2020The Journal of Clincial InvesitgationInfectious DiseaseISH/FISHHALO
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 macaquesWebb 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 JB2020PLOS PathogensInfectious DiseaseCytonuclear, ISH/FISHHALO
Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food IntakeAdriaenssens 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 F2019Cell MetabolismMetabolismISH/FISHHALO
Detection and quantification of†Parascaris†P-glycoprotein drug transporter expression with a novel mRNA hybridization techniqueChelladurai JJ, Brewer MT2019Veterinary ParasitologyInfectious DiseaseISH/FISHHALO
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 M2019EMBO ReportsOncology, Immuno-oncologyISH/FISHHALO
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 C2019PLOS OneOncology, Immuno-oncologyISH/FISHHALO
Expression of cholecystokinin by neurons in mouse spinal dorsal hornGuitierrez-Mecinas M, Bell AM, Shepherd F, Polgar E, Watanabe M, Furuta T, Todd AJ2019The Journal of Comparitive NeurologyNeuroscienceISH/FISHHALO
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-R2019Alzheimer's Research & TherapyNeuroscienceISH/FISHHALO
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 DG2019GutOncologyCytonuclear, ISH/FISHHALO
Single-Cell Quantification of mRNA Expression in The Human BrainJolly S, Lang V, Koelzer VH, Frigerio CS, Magno L, Salinas PC, Whiting P, Palomer E2019Scientific ReportsNeuroscienceISH/FISHHALO
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 2019Cell ReportsNeuroscience, MetabolismISH/FISHHALO
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 ZG2019JHEP ReportsFibrosisISH/FISHHALO
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 VK2019Scientific ReportsNeuroscienceISH/FISHHALO
Small Molecule IL-36? Antagonist as a Novel Therapeutic Approach for Plaque PsoriasisTodorovi? 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 VE2019Scientific ReportsImmunology, DermatologyISH/FISHHALO
Expression of avian ?-defensin mRNA in the chicken yolk sacZhang H, Wong EA2019Developmental & Comparative ImmunologyImmunologyISH/FISHHALO
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 SJ2018Science Translational MedicineMetabolismISH/FISHHALO
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 JC2018CellNeuroscience, MetabolismISH/FISHHALO
Gene Signature of Proliferating Human Pancreatic ?-CellsDominguez Gutierrez G, Xin Y, Okamoto H, Kim J, Lee A-H, Ni M, Adler C, Yancopoulos GD, Murphy AJ, Gromada J2018EndocrionologyMetabolismISH/FISHHALO
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 DE2018Investigational New DrugsOncologyISH/FISHHALO
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 cytometryGuo L, Wang Z, Anderson CA, Doolittle E, Kernag S, Cotta CV, Ondrejka SL, Ma X-J, Cook JR2018Modern PathologyOtherClassifier, ISH/FISHHALO
Mutant myocilin impacts sarcomere ultrastructure in mouse gastrocnemius muscle Lynch JM, Dolman AJ, Guo C, Dolan K, Xiang C, Reda S, Li B, Prasanna G2018PLOS OneGastroenterology, MyologyISH/FISHHALO
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 DG2018Nature CommunicationsOncology, Immuno-oncologyISH/FISHHALO
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 BW2017PLOS OneOncologyISH/FISHHALO
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 D2017Annals of OncologyOncology Classifier, ISH/FISHHALO
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 H2016Journal of Cellular BiochemistryOncology, Gastroenterology, Infectious DiseaseISH/FISHHALO
Variability in Platelet-Derived Growth Factor Receptor Alpha Antibody Specificity May Impact Clinical Utility of Immunohistochemistry AssaysHolzer TR, Reising LO, Credille KM, Schade AE, Oakley2016Journal of Histochemistry & CytochemistryOncologyCytonuclear, ISH/FISHHALO
Differential Cytokine Gene Expression in Granulomas from Lungs and Lymph Nodes of Cattle Experimentally Infected with Aerosolized Mycobacterium bovis Palmer MV, Thacker TC, Waters WR2016PLOS OneInfectious DiseaseISH/FISHHALO
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 J2016Cell MetabolismMetabolismISH/FISHHALO
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 RD2015NatureMetabolismISH/FISHHALO
Activation of the renal GLP?1R leads to expression of Ren1 in the renal vascular treeBj¯rnholm KD, Ougaard ME, Skovsted GF, Knudsen LB, Pyke C2021Endocrinology, Diabetes, & MetabolismMetabolismISH/FISHHALO
A Method to Pre-Screen Rat Mammary Gland Whole-Mounts Prior To RNAscopeDuderstadt EL, Sanders MA, Samuelson DJ2021Journal of Mammary Gland Biology and NeoplasiaISH/FISHHALO
Age-associated expression of p21and p53 during human wound healingChia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L2021Aging CellDermatologyArea Quantification, ISH/FISH, Multiplex IHCHALO
Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cellsNewman AC, Falcone M, Uribe AH, Zhang T, Athineos D, Pietzke M, Vazquez A, Blyth K, Maddocks ODK2021Molecular CellImmuno-oncologyClassifier, ISH/FISHHALO
VGLUT2 is a determinant of dopamine neuron resilience in a rotenone model of dopamine neurodegenerationBuck SA, De Miranda BR, Logan RW, Fish KN, Greenamyre JT, Freyberg Z2021The Journal of NeuroscienceNeuroscienceISH/FISHHALO
Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaquesBochart 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 JV2021PLOS PathogensInfectious DiseaseISH/FISH, Multiplex IHCHALO
Mucosal IFNγ production and potential role in protection in Escherichia coli O157:H7 vaccinated and challenged cattleSchaut RG, Palmer MV, Boggiatto PM, Kudva IT, Loving CL, Sharma VK2021Scientific ReportsImmunologyISH/FISHHALO
Functionally distinct POMC-expressing neuron subpopulations in hypothalamus revealed by intersectional targetingBiglari 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 JC2021Nature NeuroscienceNeuroscienceISH/FISHHALO
Oncogenic BRAF, unrestrained by TGF?-receptor signalling, drives right-sided colonic tumorigenesisLeach J, Vlahov N, Tsantoulis P, et al2021Nature CommunicationsOncologyISH/FISH, Highplex FLHALO
Lawsonia intracellularis infected enterocytes lack sucrase-isomaltase which contributes to†reduced pig digestive capacityHelm E, Burrough E, Leite, F, Gabler, N2021Veterinary ResearchOtherISH/FISHHALO
Mechanism of Nucleic Acid Sensing in Retinal Pigment Epithelium (RPE): RIG-I Mediates Type I Interferon Response in Human RPESchustak J, Twarog M, Wu X, Huang Q, Bao Y2021Journal of Immunology ResearchArea Quantification, ISH/FISHHALO
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancerNajumudeen 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 OJ2021Nature GeneticsOncologyISH/FISHHALO
Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8+ cellsMcBrien 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 G2020NatureOtherISH/FISHHALO
CTLA-4 and PD-1 dual blockade induces SIV reactivation without control of rebound after antiretroviral therapy interruptionHarper 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, Paiardini2020Nature MedicineImmunology, Infectious DiseaseCytonuclear, ISH/FISHHALO
HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cellsWang 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 J2020Nature ImmunologyImmunology, Infectious DiseaseArea Quantification, Cytonuclear, ISH/FISHHALO
Glucagon Receptor Inhibition Reduces Hyperammonemia and Lethality in Male Mice with Urea Cycle DisorderCavino K, Sung B, Su Q, Na E, Kim J, Cheng X, Gromada J, Okamoto H2020EndocrinologyMetabolismISH/FISH, Multiplex IHCHALO
Chronic stress differentially alters mRNA expression of opioid peptides and receptors in the dorsal hippocampus of female and male ratsJohnson MA, Contoreggi NH, Kogan JF, Bryson M, Rubin BR, Gray JD, Kreek MJ, McEwen BS, Milner TA2021The Journal of Comparative NeurologyNeruoscienceISH/FISHHALO
Monocyte and macrophage derived myofibroblasts: Is it fate? A review of the current evidenceVierhout M, Ayoub A, Naiel S, Yazdanshenas P, Revill S, Reihani A, Dvorkin-Gheva A, Shi W, Ask K2021Wound Repair and RegenerationReviewISH/FISHHALO
Alteration of Colonic Mucin Composition and Cytokine Expression in Acute Swine DysenteryLin S J-H, Arruda B, Burrough E2021Veterinary PathologyImmunologyArea Quantification, ISH/FISHHALO
Orexin receptors 1 and 2 in serotonergic neurons differentially regulate peripheral glucose metabolism in obesityXiao 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.2021Nature CommunicationsMetabolismISH/FISHHALO
Three subtypes of lung cancer fibroblasts definedistinct therapeutic paradigmsHu 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 J2021Cancer CellOncologyCytonuclear, ISH/FISHHALO
Functional heterogeneity of POMC neurons relies on mTORC1 signalingSaucisse 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 D2021Cell ReportsNeuroscienceISH/FISHHALO
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
Transcriptomic analysis links diverse hypothalamic cell types to fibroblast growth factor 1-induced sustained diabetes remissionBentsen 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 TH2020Nature CommunicationsMetabolismISH/FISHHALO
PPAR-gamma induced AKT3 expression increases levels of mitochondrial biogenesis driving prostate cancerGalbraith L, Mui E, Nixon C, Hedley A, Strachan D, MacKay G, Sumpton D, Sansom O, Leung H, Ahmad I2021OncogeneOncologyISH/FISHHALO
Cross-Platform Comparison of Computer-assisted Image Analysis Quantification of In Situ mRNA Hybridization in Investigative PathologyHolzer TR, Hanson JC, Wray EM, Bailey JA, Kennedy KR, Finnegan PR, Nasir A, Credille KM2019Applied Immunohistochemistry & Molecular MorpholgyOtherISH/FISHHALO
EBV+†tumors exploit tumor cell-intrinsic and -extrinsic mechanisms to produce regulatory T cell-recruiting chemokines CCL17 and CCL22Jorapur 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 G2022PLOS PathogensOncologyISH/FISHHALO
AAV9/MFSD8 gene therapy is effective in preclinical models of neuronal ceroid lipofuscinosis type 7 diseaseChen X, Dong T, Hu Y, Shaffo F, Belur N, Mazzulli J, Gray S2022The Journal of Clinical InvestigationNeuroscienceArea Quantification, ISH/FISHHALO
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 D2022Research SquareInfectious Disease, OtherISH/FISHHALO
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 lifeBrand M, Proctor A, Hostetter J, Zhou N, Friedberg I, Jergens A, Phillips G, Wannemuehler M2022PLOS ONEOtherISH/FISHHALO
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
TGF?1 Induces Senescence and Attenuated VEGF Production in Retinal PericytesAvarmovic D, Archaimbault S, Kemble A, Gruener S, Lazendic M, Westenskow P2022BiomedicinesOtherISH/FISHHALO
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
Distinct Encoding of Reward and Aversion by Peptidergic BNST Inputs to the VTASoden M, Yee J, Cuevas B, Rastani A, Elum J, Zweifel L2022Frontiers in Neural CircuitsNeuroscienceISH/FISHHALO
Age-associated expression of p21 and p53 during human wound healingChia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L2021Aging CellDermatologyArea Quantification, ISH/FISH, Multiplex IHCHALO
Hyperpolarised†13C-MRI identifies the emergence of a glycolytic cell population within intermediate-risk human prostate cancerSushentsev 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 F2022Nature CommunicationsOncologyISH/FISH, Membrane, Multiplex IHCHALO
Adult re-expression of IRSp53 rescues NMDA receptor function and social behavior in IRSp53-mutant miceNoh Y, Yook C, Kang J, Lee S, Kim Y, Yang E, Kim H, Kim E2022Communications BiologyNeuroscienceISH/FISH, Figure MakerHALO
The NALCN channel regulates metastasis and nonmalignant cell disseminationRahrmann 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 R2022Nature GeneticsOncologyISH/FISH, Multiplex IHCHALO
Relaxin/insulin-like family peptide receptor 4 (Rxfp4) expressing hypothalamic neurons Q8 modulate food intake and preference in miceLewis 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 F2022Molecular MetabolismMetabolismISH/FISH, Highplex FLHALO
Regional epithelial cell diversity in the small intestine of pigsWiarda J, Becker S, Sivasankaran S, Loving C, 2022Journal of Animal ScienceGastroenterologyISH/FISH, Figure MakerHALO
Single cell analysis of cribriform prostate cancer reveals cell intrinsic and tumor microenvironmental pathways of aggressive diseaseWong 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 P2022Nature CommunicationsOncologyISH/FISHHALO
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
Transcriptional and functional divergence in lateral hypothalamic glutamate neurons projecting to the lateral habenula and ventral tegmental areaRossi M, Basiri M, Liu Y, Hashikawa Y, Hashikawa K, Fenno L, Kim Y, Ramakrishnan C, Deisseroth K, Stuber G2021NeuronNeuroscienceISH/FISHHALO
Genetic suppression of the dopamine D3 receptor in striatal D1 cells reduces the development of L-DOPA-induced dyskinesiaLanza K, Centner A, Coyle M, Del Priore I, Manfredsson F, Bishop C2021Experimental NeurologyNeuroscienceISH/FISHHALO
An endogenous opioid circuit determines state-dependent reward consumptionCastro D, Oswell C, Zhang E, Pedersen C, Piantadosi S, Rossi M, Hunker A, Guglin A, Moron J, Zweifel L, Stuber G, Bruchas M2021NatureNeuroscienceISH/FISHHALO
Sex differences in the rodent hippocampal opioid system following stress and oxycodone associated learning processesChalangal J, Mazid S, Windisch K, Milner T2021Pharmacology Biochemistry and BehaviorReviewISH/FISHHALO
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
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 J2021The Journal of ImmunologyImmuno-oncology, otherISH/FISHHALO
A single-cell atlas of mouse lung developmentNegretti 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 J2021DevelopmentOtherISH/FISHHALO
Glutaminase 2 Knockdown Reduces Hyperammonemia and Associated Lethality of Urea Cycle Disorder Mouse ModelMao X, Chen H, Lin A, Kim S, Burczynski M, Na E, Halasz G, Sleeman M, Murphy A, Okamoto H, Cheng X2022Journal of Inherited Metabolic DiseaseMetabolismArea Quantification, ISH/FISHHALO
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 Z2022European UrologyOtherArea Quantification, ISH/FISHHALO
Adolescent intermittent ethanol exposure produces Sex-Specific changes in BBB Permeability: A potential role for VEGFAVore A, Barney T, Deak M, Varlinskaya E, Deak T2022Brain, Behavior, and ImmunityNeuroscienceISH/FISHHALO
Relationship between impaired BMP signalling and clinical risk factors at early-stage vascular injury in the preterm infantHeydarian 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 A2022ThoraxOtherISH/FISHHALO
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
Spatiotemporal expression pattern of Progesterone Receptor Component (PGRMC) 1 in endometrium from patients with or without endometriosis or adenomyosisThieffry C, Van Wynendaele M, Samain L, Tyteca D, Pierreux C, Marbaix E, Henriet P2022The Journal of Steroid Biochemistry and Molecular BiologyOtherISH/FISH, Highplex FLHALO, 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 PrimatesDevanathan 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 A2022Antimicrobial Agents and ChemotherapyInfectious DiseaseISH/FISHHALO
CD123-directed allogeneic chimeric-antigen receptor T-cell therapy (CAR-T) in blastic plasmacytoid dendritic cell neoplasm (BPDCN): Clinicopathological insightsPemmaraju 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 M2022Leukemia ResearchImmuno-oncologyISH/FISHHALO
Localization of macrophage subtypes and neutrophils in the prostate tumor microenvironment and their association with prostate cancer racial disparitiesMaynard J, Godwin T, Lu J, Vidal I, Lotan T, De Marzo A, Joshu C, Sfanos K2022The ProstateOncologyISH/FISH, Multiplex IHCHALO
Molecular identification of spatially distinct anabolic responses to mechanical loading in murine cortical boneChlebek C, Moore J, Ross F, van der Meulen M2022Journal of Bone and Mineral ResearchOtherISH/FISHHALO
Sex-specific effects of ethanol consumption in older Fischer 344 rats on microglial dynamics and A_(1-42) accumulationMarsland P, Vore A, DaPrano E, Paluch J, Blackwell A, Varlinskaya E, Deak T2022AlcoholNeuroscienceISH/FISHHALO
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 miceWoods C, Contoreggi N, Johnson M, Milner T, Wang G, Glass M, 2022Neurochemistry InternationalNeuroscienceISH/FISHHALO
Angiotensin II Infusion Results in Both Hypertension and Increased AMPA GluA1 Signaling in Hypothalamic Paraventricular Nucleus of Male but not Female MiceWang G, Woods C, Johnson M, Milner T, Glass M2022NeuroscienceNeuroscienceISH/FISHHALO
Multiregional single-cell dissection of tumor and immune cells reveals stable lock-and-key features in liver cancerMa 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 X2022Nature CommunicationsOncologyISH/FISHHALO
Autologous T cell therapy for MAGE-A4+ solid cancers in HLA-A*02+ patients: a phase 1 trialHong 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 M2023Nature MedicineImmuno-oncologyISH/FISH, Spatial Analysis, Highplex FLHALO
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
Combined KRASG12C and SOS1 inhibition enhances and extends the anti-tumor response in KRASG12C-driven cancers by addressing intrinsic and acquired resistanceThatikonda 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 M2023bioRxivOncologyISH/FISH, Multiplex IHC, Highplex FL, Figure MakerHALO
Prefrontal cortical protease TACE/ADAM17 is involved in neuroinflammation and stress-related eating alterationsSharafeddin F, Ghaly M, Simon T, Ontiveros-Angel P, Figueroa J2023bioRxivNeuroscienceISH/FISHHALO
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 J2023Research SquareOncologyISH/FISHHALO
CD47-Dependent Regulation of Immune Checkpoint Gene Expression and MYCN mRNA Splicing in Murine CD8 and Jurkat T CellsKaur S, Awad D, Finney R, Meyer T, Singh S, Cam M, Karim B, Warner A, Roberts D2023International Journal of Molecular SciencesImmuno-oncologyISH/FISHHALO
IL17A mRNA staining distinguishes palmoplantar psoriasis from hyperkeratotic palmoplantar eczema in diagnostic skin biopsiesChen J, Murphy M, Singh K, Wang A, Chow R, Kim S, Cohen J, Ko C, Damsky W2023JID InnovationsDermatologyISHHALO
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 mannerMahadevan 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 R2023bioRxivOncologyFISH, Highplex FLHALO
In-depth virological and immunological characterization of HIV-1 cure after CCR5Δ32/Δ32 allogeneic hematopoietic stem cell transplantationJensen 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 G2023Nature MedicineInfectious DiseaseISH, Figure MakerHALO
Lorazepam stimulates IL-6 production and is associated with poor survival outcomes in pancreatic cancerCornwell 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 M2023medrxivOncologyFISH-IFHALO
Myeloid-specific deletion of activating transcription factor 6 alpha increases CD11b+ macrophage subpopulations and aggravates lung fibrosisMekhael 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 K2023Immunology and Cell BiologyImmunology, FibrosisClassifier, Area Quantification, FISH, Multiplex IHCHALO
Metabolic profiling stratifies colorectal cancer and reveals adenosylhomocysteinase as a therapeutic targetVoorde 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 O2023bioRxivOncologyISHHALO
SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescenceGioia 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 F2023Nature Cell BiologyInfectious DiseaseISH/FISH, Highplex FLHALO
Tyrosinase-induced neuromelanin accumulation triggers rapid dysregulation and degeneration of the mouse locus coeruleusIannitelli A, Segal A, Pare J, Mulvey B, Liles L, Sloan S, McCann K, Dougherty J, Smith Y, Weinshenker D2023bioRxivNeuroscienceFISH-IFHALO
Cellular mechanisms of heterogeneity in NF2-mutant schwannomaChiasson-MacKenzie C, Vitte J, Liu C, Wright E, Flynn E, Stott S, Giovannini M, McClatchey A2023Nature CommunicationsOncologyClassifier, Multiplex IHC, Spatial Analysis, FISH-IFHALO
Pseudoknot-targeting Cas13b combats SARS-CoV-2 infection by suppressing viral replicationYu D, Han H, Yu J, Kim J, Lee G, Yang J, Song B, Tark D, Choi B, Kang S, Heo W2023Molecular TherapyInfectious DiseaseISH, FISH-IFHALO
Chronic immune activation and gut barrier dysfunction is associated with neuroinflammation in ART-suppressed SIV+ rhesus macaquesByrnes 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 M2023PLOS PathogensInfectious DiseaseArea Quantification, Object Colocalization, ISH, Highplex FLHALO
Dedifferentiation maintains melanocyte stem cells in a dynamic nicheSun 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 M2023NatureOtherFISHNature
Adrenal cortex size and homeostasis are regulated by gonadal hormones via androgen receptor/β-catenin signaling crosstalkLyraki R, Grabek A, Tison A, Weerasinghe-Arachchige L, Peitzsch M, Bechman N, Youssef S, de Bruin A, Bakker E, Claessens F, Chaboissier M, Schedl A2023Disease Models & MechanismsOtherFISH, Highplex FLHALO
Neural mechanism of acute stress regulation by trace aminergic signalling in the lateral habenula in male miceYang 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 H2023Nature CommunicationsNeuroscienceFISHHALO
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
D-serine availability modulates prefrontal cortex inhibitory interneuron development and circuit maturationFolorunso O, Brown S, Baruah J, Harvey T, Jami S, Radzishevsky I, Wolosker H, McNally J, Gray J, Vasudevan A, Balu D2023Scientific ReportsNeuroscienceISHHALO
Kv7/KCNQ potassium channels in cortical hyperexcitability and juvenile seizure-related death in Ank2-mutant miceOh 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 E2023Nature CommunicationsNeuroscienceFISHHALO
A cellular and molecular spatial atlas of dystrophic muscleStec 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 M2023Proceedings of the National Academy of SciencesMyologyISH/FISH, Highplex FLHALO
Localization of unlabelled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imagingSpencer-Dene B, Mukherjee P, Alex A, Bera K, Tseng W, Shi J, Chaney E, Spillman Jr. D, Marjanovic B, Miranda E, Boppart S, Hood S2023RNAOtherISHHALO, HALO AI
Long-Term Dysfunction of Taste Papillae in SARS-CoV-2Yao Q, Doyle M, Liu Q, Appleton A, O'Connell J, Weng N, Egan J2023NEJM EvidenceInfectious DiseaseFISHHALO
LINC01638 Sustains Human Mesenchymal Stem Cell Self-Renewal and Competency for Osteogenic Cell FateGordon J, Tye C, Banerjee B, Ghule P, Wijnen A, Kabala F, Page N, Falcone M, Stein J, Stein G, Lian J2023Research SquareOtherObject Colocalization, FISHHALO
HIF-1 regulates pathogenic cytotoxic T cells in lupus skin diseaseLittle A, Chen P, Vesely M, Khan R, Fiedler J, Garritano J, Maisha F, McNiff J, Craft J2023JCI InsightImmunology, DermatologyFISH-IFHALO, HALO AI
ABCC2 brush-border expression predicts outcome in papillary renal cell carcinoma: a multi-institutional study of 254 casesCastillo 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 RM2023HistopathologyOncologyISHHALO
Single-cell analysis of the miRNA activities in tuberculous meningitis (TBM) model mice injected with the BCG vaccineZhang X, Pan L, Zhang P, Wang L, Shen Y, Xu P, Ren Y, Huang W, Liu P, Wu Q, Li F2023International ImmunopharmacologyInfectious DiseaseFISHHALO
Osteoprogenitor recruitment and differentiation during intracortical bone remodeling of adolescent humansChristiansen PvD, Andreasen CM, El-Masri BM, Laursen KS, Delaisse JM, Andersen TL2023BoneOtherFISHHALO, HALO AI
Characterization of expression and prognostic implications of transforming growth factor beta, programmed death-ligand 1, and T regulatory cells in canine histiocytic sarcomaMurphy J, Shiomitsu K, Milner R, Lejeune A, Ossiboff R, Gell J, Axiak-Bechtel S2023Veterinary Immunology and ImmunopathologyOncologyISHHALO
Baseline skin cytokine profiles determined by RNA in situ hybridization correlate with response to dupilumab in patients with eczematous dermatitisSingh K, Valido K, Swallow M, Okifo K, Wang A, Cohen J, Damsky W2023Journal of the American Academy of DermatologyDermatologyISHHALO
FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cellsDanopoulos S, Belgacemi R, Hein R, Miller A, Deutsch G, Glass I, Spence J, Al Alam D2023American Journal of Physiology - Lung Cellular and Molecular PhysiologyOtherFISHHALO
A Spatial Atlas of Wnt Receptors in Adult Mouse LiverGayden J, Hu S, Joseph P, Delgado E, Liu S, Bell A, Puig S, Monga S, Freyberg Z2023The American Journal of PathologyGastroenterologyFISHHALO
Vascular-Parenchymal Crosstalk Promotes Lung Fibrosis Through BMPR2 SignalingYanagihara 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 M2023American Journal of Respiratory and Critical Care MedicineFibrosisArea Quantification, ISH, TMAHALO
Intrinsic BMP inhibitor Gremlin regulates alveolar epithelial type II cell proliferation and differentiationYanagihara T, Zhou Q, Tsubouchi K, Revill S, Ayoub A, Gholiof M, Chong S, Dvorkin-Gheva A, Ask K, Shi W, Kolb M2023Biochemical and Biophysical Research CommunicationsOtherISH, TMAHALO
Characterization of expression and prognostic implications of GD2 and GD3 synthase in canine histiocytic sarcomaMurphy J, Axiak-Bechtel S, Milner R, Lejeune A, Ossiboff R, Castellanos Gell J, Shiomitsu K2023Veterinary Immunology and ImmunopathologyOncologyISHHALO
Genetically- and spatially-defined basolateral amygdala neurons control food consumption and social interactionLim H, Zhang Y, Peters C, Straub T, Mayer JL, Klein R2023bioRxivNeuroscienceFISHHALO
Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissueHuuki-Myers L, Montgomery KD, Kwon SH, Page SC, Hicks SC, Maynard KR, Collado-Torres L2023Genome BiologyOtherFISH-IFHALO
Prednisolone and rapamycin reduce the plasma cell gene signature and may improve AAV gene therapy in cynomolgus macaquesKistner 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 A2023Gene TherapyOtherFISH-IFHALO
CRISPR–Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading framesZheng 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 Y2023Nature Structural & Molecular BiologyOncologyISHHALO
Entorhinal cortex vulnerability to human APP expression promotes hyperexcitability and tau pathologyRowan M, Goettemoeller A, Banks E, McCann K, Kumar P, South K, Olah V, Ramelow C, Duong D, Seyfried N, Rangaraju S, Weinshenker D2023Research SquareNeuroscienceFISH-IFHALO
mRNA Vaccine Trafficking and Resulting Protein Expression After Intramuscular AdministrationHassett KJ, Rajilic IL, Bahl K, White R, Cowens K, Jacquinet E, Burke KE2023Molecular Therapy: Nucleic AcidOtherISH, Multiplex IHCHALO
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 trialLee E, Coulter J, Mishra A, Caramella-Pereira F, Demarzo A, Rudek M, Hu C, Han M, DeWeese TL, Yegnasubramanian S, Song DY2023TrialsOncologyObject Colocalization, ISHHALO
Detection of IL12/23p40 via PET Visualizes Inflammatory Bowel DiseaseRezazadeh F, Ramos N, Saliganan A, Al-Hallak N, Chen K, Mohamad B, Wiesend W, Viola N2023Journal of Nuclear MedicineImmunologyISHHALO
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 J2023Molecular Cancer ResearchOncologyFISHHALO
Spatial Transcriptomics Reveals Distinct Tissue Niches Linked with Steroid Responsiveness in Acute Gastrointestinal GVHDPatel BK, Raabe MJ, Lang ER, Song Y, Lu C, Deshpande V, Nieman LT, Aryee MJ, Chen YB, Ting DT, DeFilipp Z2023BloodImmunologyISHHALO
Ventral pallidum neurons projecting to the ventral tegmental area reinforce but do not invigorate reward-seeking behaviorPalmer D, Cayton CA, Scott A, Lin I, Newell B, Paulson A, Weberg M, Richard JM2024Cell ReportsNeuroscienceFISHHALO
Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitisMennillo 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 G2024Nature CommunicationsImmunologyISH, Spatial Analysis, Highplex FL, TMAHALO, 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 J2024Kidney InternationalOtherISH, Spatial Analysis, Highplex FLHALO, HALO AI
N6-methyladenosine-modified circSLCO1B3 promotes intrahepatic cholangiocarcinoma progression via regulating HOXC8 and PD-L1Li J, Xu X, Xu K, Zhou X, Wu K, Yao Y, Liu Z, Chen C, Wang L, Sun Z, Jiao D, Han X2024Journal of Experimental & Clinical Cancer ResearchOncologyArea Quantification, FISH, Highplex, TMAHALO
A First-in-Human Phase 1 Study of a Tumor-Directed RNA-Interference Drug against HIF2a in Patients with Advanced Clear Cell Renal Cell CarcinomaBrugarolas 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 M2024Clinical Cancer ResearchOncologyISHHALO
High-resolution and quantitative spatial analysis reveal intra-ductal phenotypic and functional diversification in pancreatic cancerMichiels 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 I2024Journal of PathologyOncologySpatial Analysis, FISH-IFHALO
Spatial distribution of Mycobacterium tuberculosis mRNA and secreted antigens in acid-fast negative human antemortem and resected tissueNargan K, Glasgow J, Nadeem S, Naidoo T, Wells G, Hunter R, Hutton A, Lumamba K, Msimang M, Benson P, Steyn A2024EBioMedicineInfectious DiseaseArea Quantification, ISHHALO
Spatial multi-omics of human skin reveals KRAS and inflammatory responses to spaceflightPark 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 E2024Nature CommunicationsDermatologyISHHALO
Adjuvant COX inhibition augments STING signaling and cytolytic T cell infiltration in irradiated 4T1 tumorsRidnour 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 D2024JCI InsightImmuno-oncologyClassifier, FISH, Spatial Analysis, Highplex FLHALO
Development of NR0B2 as a therapeutic target for the re-education of tumor associated myeloid cellsVidana 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 R2024Cancer LettersOncologyISH, Multiplex IHCHALO
Co-targeting SOS1 enhances the antitumor effects of KRASG12C inhibitors by addressing intrinsic and acquired resistanceThatikonda 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 H2024Nature CancerOncologyFISH, Highplex FLHALO
Metabolic imaging across scales reveals distinct prostate cancer phenotypesSushentsev 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 A2024Nature CommunicationsOncologyArea Quantification, FISH, Membrane, Multiplex IHCHALO, HALO AI
Genetically- and spatially-defined basolateral amygdala neurons control food consumption and social interactionLim H, Zhang Y, Peters C, Straub T, Luise Mayer J, Klein R2024Nature CommunicationsNeuroscienceFISHHALO
A γδ T cell–IL-3 axis controls allergic responses through sensory neuronsFlayer 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 L2024NatureNeuroscienceArea Quantification, FISH-IFHALO, HALO AI
Non-human primate model of long-COVID identifies immune associates of hyperglycemiaPalmer 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 J2024Nature CommunicationsInfectious DiseaseISH, Highplex FLHALO
Mapping RANKL- and OPG-expressing cells in bone tissue: the bone surface cells as activators of osteoclastogenesis and promoters of the denosumab rebound effectEl-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 L2024Bone ResearchMyologyISH, Spatial AnalysisHALO, 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

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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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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