Indica
Backed by cutting edge technology, an uncompromising focus on ease-of-use and dedicated customer service, Indica Labs’ software and services are being used to make vital discoveries in pathology labs and research organizations around the world.

Multiplex FISH

MULTIPLEX FISH

(Designed for Fluorescent RNAscope®)

 

Product Overview

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


Watch a webinar from two of our customers discussing how they use and analyze RNAscope assays in their research and download the full ACD Bio™ RNAscope Data Analysis Guide by clicking the links here.


In the example above the module measures a two-plex RNAscope assay on pelleted cancer cells. Single cells are identified using the nuclear dye DAPI. The multiplexed red and green probes are measured within the cell boundaries (spots per cell and probe area per cell). The module reports the average number of each probe per cell or across the entire region of analysis. In the analysis markup image, cells positive for the red probe alone are highlighted in different shades of red, cells positive for the green probe alone in different shades of green and cells positive for both probes are highlighted in shades of yellow. The color shading is determined by the number of probes and the corresponding RNAscope H-score, dark color = lower expression and light color = higher expression.

The Multiplex FISH module integrates seamlessly into the HALO® platform which is compatible with a number of third party systems and  file formats.

Contact info@indicalab.com for product demonstration and pricing information or upload some images for a free trial.

MULTIPLEX FISH

(Designed for RNAscope®)

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


Watch a webinar from two of our customers discussing how they use and analyze RNAscope assays in their research and download the full ACD Bio™ RNAscope Data Analysis Guide by clicking the links here.


In the example above the module measures a two-plex RNAscope assay on pelleted cancer cells. Single cells are identified using the nuclear dye DAPI. The multiplexed red and green probes are measured within the cell boundaries (spots per cell and probe area per cell). The module reports the average number of each probe per cell or across the entire region of analysis. In the analysis markup image, cells positive for the red probe alone are highlighted in different shades of red, cells positive for the green probe alone in different shades of green and cells positive for both probes are highlighted in shades of yellow. The color shading is determined by the number of probes and the corresponding RNAscope H-score, dark color = lower expression and light color = higher expression.

HALO is compatible with a broad spectrum of image and digital slide formats.  Yours not on the list? Email us your requirements.

Non-proprietary (JPG, TIF)
Nikon (ND2)
3D Histech (MRXS)
Perkin Elmer (QPTIFF, component TIFF)
Olympus (VSI)
Hamamatsu (NDPI, NDPIS)
Aperio (SVS, AFI)
Zeiss (CZI)
Leica (SCN, LIF)
Philips (Requires Philips IMS)

Quantitative RNAscope®️ Image Analysis Guide.

PUBLICATIONS

Here are a few publications that cite use of our ISH and FISH modules.  Your publication not on the list?  Drop us an email to let us know about it!

TitleAuthorsYearJournalApplicationHALO Modules
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/FISH
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/FISH
TGFβ inhibition restores a regenerative response in acute liver injury by suppressing paracrine senescence Bird TG, Müller 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/FISH
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, Günther S, Langer T, Rahmouni K, Fenselau H, Krüger M, Brüning JC2018CellNeuroscience, MetabolismISH/FISH
Detection and quantification of Parascaris P-glycoprotein drug transporter expression with a novel mRNA hybridization techniqueChelladurai JJ, Brewer MT2019Veterinary ParasitologyInfectious DiseaseISH/FISH
IL-7-dependent compositional changes within the γδ 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/FISH
Gene Signature of Proliferating Human Pancreatic α-CellsDominguez Gutierrez G, Xin Y, Okamoto H, Kim J, Lee A-H, Ni M, Adler C, Yancopoulos GD, Murphy AJ, Gromada J2018EndocrionologyMetabolismISH/FISH
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/FISH
APNG as a prognostic marker in patients with glioblastoma Fosmark S, Hellwege S, Dahlrot RH, Jensen KL, Derand H, Lohse J, Sørensen MD, Hansen S, Kristensen BW2017PLOS OneOncologyISH/FISH
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/FISH
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/FISH
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/FISH
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/FISH
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 PathologyClassifier, ISH/FISH
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/FISH
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/FISH
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/FISH
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/FISH
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/FISH
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/FISH
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/FISH
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/FISH
Gene expression of prostaglandin EP4 receptor in three canine carcinomasMusser ML, Viall AK, Phillips RL, Hostetter JM, Johannes CM2020BMC Veterinary ResearchOncologyISH/FISH
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/FISH
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/FISH
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/FISH
The Fat Mass and Obesity-Associated Protein (FTO) Regulates Locomotor Responses to Novelty via D2R Medium Spiny Neurons Ruud J, Alber J, Tokarska A, Engström Ruu L, Nolte H, Biglari N, Lippert R, Lautenschlager Ä, Cieślak PE, Szumiec Ł, Hess ME, Brönneke HS, Krüger M, Nissbrandt H, Korotkova T, Silberberg G, Rodriguez Parkitna J, Brüning J2019Cell ReportsNeuroscience, MetabolismISH/FISH
NPY mediates the rapid feeding and glucose metabolism regulatory functions of AgRP neuronsRuud LE, Pereira MMA, de Solis AJ, Fenselau H, Bruning JC2020Nature CommunicationsMetabolismISH/FISH
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/FISH
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/FISH
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/FISH
Small Molecule IL-36γ Antagonist as a Novel Therapeutic Approach for Plaque PsoriasisTodorović 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/FISH
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 OncologyOncologyClassifier, ISH/FISH
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/FISH
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/FISH
Expression of avian β-defensin mRNA in the chicken yolk sacZhang H, Wong EA2019Developmental & Comparative ImmunologyImmunologyISH/FISH
Activation of the renal GLP‐1R leads to expression of Ren1 in the renal vascular treeBjørnholm KD, Ougaard ME, Skovsted GF, Knudsen LB, Pyke C2021Endocrinology, Diabetes, & MetabolismMetabolismISH/FISH
A Method to Pre-Screen Rat Mammary Gland Whole-Mounts Prior To RNAscopeDuderstadt EL, Sanders MA, Samuelson DJ2021Journal of Mammary Gland Biology and NeoplasiaISH/FISH
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 IHC
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/FISH
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/FISH
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 IHC
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/FISH
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, Klöckener T, Sotelo-Hitschfeld T, Abbasloo A, Edenhofer F, Reimann F, Gribble FM, Fenselau H, Kloppenburg P, Wunderlich FT, Brüning JC2021Nature NeuroscienceNeuroscienceISH/FISH

Use the form below to upload up to three images for us to analyze using HALO.  If the form does not display, please click here.