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HALO® Module

TMA (Tissue Microarray) Add-On

The TMA add-on provides a productivity-enhancing workflow for tissue microarray analysis by enabling automated, high-throughput, segmentation and batch analysis of whole slide TMA images.  The add-on can be used in conjunction with any of our cell-based analysis modules for brightfield or fluorescence, as well as our tissue classifier add-on for automated tumor detection.  In combination, these tools allow the user to automatically identify tumor, and quantify cell-based IHC, ISH, or Immunofluorescence assays within just the relevant tumor regions; eliminating the need for manual exclusion of non-tumor regions.

File formats supported by the HALO image analysis platform:

  • Non-proprietary (JPG, TIF, OME.TIFF)
  • Nikon (ND2)
  • 3D Histech (MRXS)
  • Akoya (QPTIFF, component TIFF)
  • Olympus / Evident (VSI)
  • Hamamatsu (NDPI, NDPIS)
  • Aperio (SVS, AFI)
  • Zeiss (CZI)
  • Leica (SCN, LIF)
  • Ventana (BIF)
  • Philips (iSyntax, i2Syntax)
  • DICOM (DCM*)
    *whole-slide images

Publication Spotlight

The table below includes publications that cite the TMA (Tissue Microarray) Add-on. 

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

TitleAuthorsYearJournalApplicationHALO ModulesProduct
Linking epigenetic signature and metabolic phenotype in IDH mutant and IDH wildtype diffuse gliomaBuran Y, Filipski K, Bernatz S, Baumgarten P, Roller B, Zinke J, Zeiner PS, Ilina E, Senft C, Ronellenfitsch MW, Plate KH, B‰hr O, Hattingen E, Steinbach JP, Mittelbron M, Harter PN2020Neuropathology and Applied NeurobiologyNeuroscienceMultiplex IHC, TMAHALO
The role of WNT10B in normal prostate gland development and prostate cancerMadueke I, Hu W-Y, Hu D, Swanson SM, Griend DV, Abern M, Prins GS2019The ProstateOncologyMultiplex IHC, TMAHALO
Tumor cell PD-L1 expression is a strong predictor of unfavorable prognosis in immune checkpoint therapy-naive clear cell renal cell cancerMˆller K, Fraune C, Blessin NC, Lennartz M, Kluth M, Hube-Magg C, Lindhorst L, Dahlem R, Fisch M, Eichenauer T, Riechardt S, Simon R, Sauter G, B¸scheck F, Hˆppner W, Matthies C, Doh O, Krech T, Marx AH, Zecha H, Rink M, Steurer S, Clauditz TS2021International Urology and NephrologyImmuno-oncologyMultiplex IHC, TMAHALO
Prognostic role of proliferating CD8+ cytotoxic Tcells in human cancersBlessin NC, Li W, Mandelkow T, Jansen HL, Yang C, Raedler JB, Simon R, B¸scheck F, Dum D, Luebke AM, Hinsch A, Mˆller K, Menz A, Bernreuther C, Lebok P, Clauditz T, Sauter G, Marx A, Uhlig R, Wilczak W, Minner S, Krech T, Fraune C, Hˆflmayer D, Burandt E, Steurer S2021Cellular OncologyImmuno-oncologyHighplex FL, TMAHALO
Tertiary lymphoid structures critical for prognosis in endometrial cancer patients - a TransPORTEC studyHoreweg N, Workel, H, Loiero D, Church D, Vermij L, LÈon-Castillo A, Krog R, de Boer S, Nout R, Powel M, Mileshkin L, MacKay H, Leary A, Singh N, J¸rgenliemk-Schulz I, Creutzberg C, Koelzer V, Nijman H, Bosse T, Bruyn M2021Research SquareMultiplex IHC, TMAHALO AI
Genomic analysis of Vascular Invasion in Hepatocellular Carcinoma (HCC) Reveals Molecular Drivers and Predictive BiomarkersKrishnan MS, Rajan KD A, Park J, Arjunan V, Marques FJG, Bermudez A, Girvan OA, Hoang NS, Yin J, Nguyen MH, Kothary N, Pitteri S, Felsher DW, Dhanasekaran R2020HepatologyOncologyMultiplex IHC, TMAHALO
T-regulatory cells predict clinical outcome in soft tissue sarcoma patients: a clinico-pathological studySmolle M, Herbsthofer L, Granegger B, Goda M, Brcic I, Bergovec M, Scheipl S, Prietl B, Pichler M, Gerger A, Rossmann C, Riedl J, Tomberger M, LÛpez-GarcÌa P, El-Heliebi A, Leithner A, Liegl-Atzwanger B, Szkandera J2021British Journal of CancerOncologyHighplex FL, TMAHALO
PIK3CA mutation and CNV status and post-chemoradiotherapy survival in patients with cervical cancerMartell K, McIntyre JB, Kornaga EN, Chan AMY, Phan T, Kobel M, Enwere EK, Dean ML, Ghatage P, Lees-Miller SP, Doll CM2020Gynecologic OncologyOncologyClassifier, Highplex FL, TMAHAO
Tissue-resident FOLR2+ macrophages associate with tumor-infiltrating CD8+ T cells and with increased survival of breast cancer patientsRamos, R, Missolo-Koussou Y, Gerber-Ferder Y, Bromley C, Bugatti M, Nunez N, Tosello J, Richer W, Denizeau J, Sedlik C, Caudana P, Kotsias F, Niborski L, Viel S, Bohec M, Lameiras S, Baulande S, Lesage L, Nicolas A, Mesure D, Vincent-Salomon A, Reyal F, Dutertre C, Ginhoux F, Vimeux L, Donnadieu E, Buttard B, Galon J, Zelenay S, Vermi W, Guermonprez P, Piaggio E, Helft J2021bioRxivImmuno-oncologyCytonuclear, Highplex FL, TMAHALO
Nuclear expression of pSTAT3Tyr705†and pSTAT3Ser727†in the stromal compartment of localized hormone-naÔve prostate cancerMarginean F, Hellsten R, Krzyanowska A, Bjartell A2022Pathology - Research and PracticeOncologyCytonuclear, Multiplex IHC, TMAHALO
Tertiary lymphoid structures critical for prognosis in endometrial cancer patients - a TransPORTEC studyHoreweg N, Workel, H, Loiero D, Church D, Vermij L, LÈon-Castillo A, Krog R, de Boer S, Nout R, Powel M, Mileshkin L, MacKay H, Leary A, Singh N, J¸rgenliemk-Schulz I, Creutzberg C, Koelzer V, Nijman H, Bosse T, Bruyn M2022Nature CommunicationsOncologyCytonuclear, Multiplex IHC, TMAHALO, HALO AI
Genomic and single-cell landscape reveals novel drivers and therapeutic vulnerabilities of transformed cutaneous T-cell lymphomaSong X, Chang S, Seminario-Vidal L, de Mingo Pulido A, Tordesillas L, Song X, Reed R, Harkins A, Whiddon S, Nguyen J, Segura C, Zhang C, Yoder S, Sayegh Z, Zhao Y, Messina J, Harro C, Zhang X, Conejo-Garcia J, Berglund A, Sokol L, Zhang J, Rodriguez P, Mule J, Futreal A, Tsai K, Chen P2022Cancer DiscoveryOncologyCytonuclear, Highplex FL, TMAHALO
Multiplex Immunohistochemical Phenotyping of T Cells in Primary Prostate CancerOzbek B, Ertunc O, Erickson A, Vidal I, Gomes-Alexandre C, Guner G, Hicks J, Jones T, Taube J, Sfanos K, Yegnasubramanian S, DeMarzo A2022The ProstateImmuno-oncologyClassifier, Cytonuclear, Highplex FL, Serial Section, Registration, Figure Maker, TMAHALO
SPOP promotes cervical cancer progress by inducing PD-1 move away from PD-L1 in spatial localizationWu J, Wu Y, Guo Q, Chen S, Wang S, Zhu J, Wu X, Ju X2022Research SquareOncologyCytonuclear, Spatial Analysis, Highplex FL, TMAHALO
Type I interferon regulates proteolysis by macrophages to prevent immunopathology following viral infectionLee A, Feng E, Chew M, Balint E, Poznanski S, Giles E, Zhang A, Marzok A, Revill S, Vahedi F, Dubey A, Ayaub E, Jimenez-Saiz R, McGrath J, Ritchie T, Jordana M, Jonigk D, Ackermann M, Ask K, Miller M, Richards C, Ashkar A2022PLOS PathogensInfectious DiseaseArea Quantification, Multiplex IHC, TMAHALO
Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial CancerHoreweg N, de Bruyn M, Nout R, Stelloo E, Kedzierska K, Leon-Castillo A, Plat A, Mertz K, Osse M, Jurgenliemk-Schulz I, Lutgens L, Jobsen J, van der Steen-Banasik E, Smit V, Creutzberg C, Bosse T, Nijman H, Koelzer V, Church D2020Cancer Immunology ResearchOncologyCytonuclear, Multiplex IHC, TMAHALO, HALO AI
Prognostic image-based quantification of CD8CD103 T cell subsets in high-grade serous ovarian cancer patientsPaijens S, Vledder A, Loiero D, Duiker E, Bart J, Hendriks A, Jalving M, Workel H, Hollema H, Werner N, Plat A, Wisman G, Yigit R, Arts H, Kruse A, de Lange N, Koelzer V, Bruyn M, Nijman H2021OncoImmunologyImmuno-oncologyCytonuclear, Multiplex IHC, TMAHALO, HALO AI
Senescence-Associated Molecules and Tumor-Immune-Interactions as Prognostic Biomarkers in Colorectal CancerKellers F, Fernandez A, Konykiewitz B, Schindeldecker M, Tagscherer K, Heintz A, Jesinghaus M, Roth W, Foersch S2022Frontiers in MedicineOncologyClassifier, Multiplex IHC, Spatial Analysis, Registration, TMAHALO
A survey on artificial intelligence in histopathology image analysisAbdelsamea M, Zidan U, Senousy Z, Gaber M, Rakha E, Ilyas M2022WIREs Data Mining and Knowledge DiscoveryReviewClassifier, Cytonuclear, Figure Maker, TMAHALO
LncRNA scaRNA2 bridges DNA end-resection to homologous recombination repair mediated chemoradioresistanceYang Y, Chen Y, Shen H, Liu T, Cao K, Wan Z, Du Z, Wang H, Yu Y, Ma S, Li B, Zhang W, Cai J, Gao F2022Research SquareOncologyHighplex FL, TMAHALO
The proteomic landscape of glioblastoma recurrence reveals novel and targetable immunoregulatory driversTatari N, Khan S, Livingstone J, Zhai K, Mckenna D, Ignatchenko V, Chokshi C, Gwynne W, Singh M, Revill S, Mikolajewicz N, Zhu C, Chan J, Hawkins C, Lu J, Provias J, Ask K, Morrissy S, Brown S, Weiss T, Weller M, Han H, Greenspoon J, Moffat J, Venugopal C, Boutros P2022Acta NeuropathologicaOncologyMultiplex IHC, Figure Maker, TMAHALO
The MK2/Hsp27 axis is a major survival mechanism for pancreatic ductal adenocarcinoma under genotoxic stressGrierson P, Dodhiawala P, Cheng Y, Chen T, Khawar I, Wei Q, Zhang D, Li L, Herndon J, Monahan J, Ruzinova M, Lim K2021Science Translational MedicineOncologyArea Quantification, TMAHALO
SIGLEC15 amplifies immunosuppressive properties of tumor-associated macrophages in pancreatic cancerLi, T, Jin K, Li H, Ye L, Li P, Jiang B, Lin X, Liao Z, Zhang H, Shi S, Lin M, Fei Q, Xiao Z, Xu H, Liu L, Yu X, Wu W2022Cancer LettersImmuno-oncologyHighplex FL, TMAHALO
Developing a Nomogram for Preoperative Prediction of Cervical Cancer Lymph Node Metastasis by Multiplex ImmunofluorescenceWu J, Guo Q, Zhu J, Wu Y, Liang S Chen S, Wang S, Ju X, Wu X2022AuthoreaOncologySpatial Analysis, Highplex FL, TMAHALO
AKR1C3 regulated by NRF2/MAFG complex promotes proliferation via stabilizing PARP1 in hepatocellular carcinomaPan D, Yang W, Zeng Y, Qin H, Xu Y, Gui Y, Fan X, Tian G, Wu Y, Sun H, Ye Y, Yang S, Zhou J, Guo Q, Zhao L2022OncogeneOncologyArea Quantification, TMAHALO
The chromatin remodeler CHD6 promotes colorectal cancer development by regulating TMEM65-mediated mitochondrial dynamics via EGF and Wnt signalingZhang B, Liu Q, Wen W, Gao H, Wei W, Tang A, Qin B, Lyu H, Meng X, Li K, Jin H, Yu F, Pan Q Lin J, Lee M2022Cell DiscoveryOncologyMultiplex IHC, TMAHALO
Low CD8 T Cell Counts Predict Benefit from Hypoxia-Modifying Therapy in Muscle-Invasive Bladder CancerSmith V, Mukherjee D, Tsakiroglou A, Baker A, Mistry H, Choudhury A, Hoskin P, Illidge T, West C2022CancersImmuno-oncologyHighplex FL, TMAHALO
NADK-mediated de novo NADP(H) synthesis is a metabolic adaptation essential for breast cancer metastasisIlter D, Drapela S, Schild T, Ward N, Adhikari E, Low V, Asara J, Oskarsson T, Lau E, DeNicola G, McReynolds M, Gomes A2023Redox BiologyOncology, MetabolismClassifier, Highplex FL, TMAHALO
PD-1+CD8+ T Cells Proximal to PD-L1+CD68+ Macrophages Are Associated with Poor Prognosis in Pancreatic Ductal Adenocarcinoma PatientsYang X, Wang G, Song Y, Zhuang T, Li Y, Xie Y, Fei X, Zhao Y, Xu D, Hu Y2023CancersOncology, Immuno-oncologyClassifier, Spatial Analysis, Highplex FL, Registration, TMAHALO
Differential expression of CD8 defines phenotypically distinct cytotoxic T cells in cancer and multiple sclerosisBurkard T, Herrero San Juan M, Dreis C, Kiprina A, Namgaladze D, Siebenbrodt K, Luger S, Foerch C, Pfeilschifter J, Weigert A, Radeke H2023Clinical and Translational MedicineOncology, immunologyClassifier, Spatial Analysis, Highplex FL, TMAHALO
The CD73 is induced by TGF-β1 triggered by nutrient deprivation and highly expressed in dedifferentiated human melanomaGiraulo C, Turiello R, Orlando L, Leonardelli S, Landsberg J, Belvedere R, Rolshoven G, Muller C, Holzel M, Morello S2023Biomedicine & PharmacotherapyOncologyHighplex FL, TMAHALO, HALO AI
ATR-binding lncRNA ScaRNA2 promotes cancer resistance through facilitating efficient DNA end resection during homologous recombination repairChen Y, Shen H, Liu T, Cao K, Wan Z, Du Z, Wang H, Yu Y, Ma S, Lu E, Zhang W, Cai J, Gao F, Yang Y2023Journal of Experimental & Clinical Cancer ResearchOncologyHighplex FL, TMAHALO
Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stabilityBenabdallah NS, Dalal V, Scott RW, Marcous F, Sotiriou A, Kommoss FKF, Pejkovska A, Gaspar L, Wagner L, Sánchez-Rivera FJ, Ta M, Thornton S, Nielsen TO, Underhill TM, Banito A2023Nature Structural & Molecular BiologyOncologyMultiplex IHC, TMAHALO, HALO AI
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
Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progressionMacke A, Pachikov A, Divita T, Morris M, LaGrange C, Holzapfel M, Kubyshkin A, Zyablitskaya E, Makalish T, Eremenko S, Qiu H, Riethoven J, Hemstreet G, Petrosyan A2023Molecular Cancer ResearchOncologyClassifier, Area Quantification, Multiplex IHC, TMAHALO

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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Multiplex IHC

Quantify expression of up to five brightfield stains in any cellular compartment - membrane, nucleus or cytoplasm.

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Highplex FL

Quantify expression of an unlimited number of biomarkers in any cellular compartment - membrane, nucleus or cytoplasm.

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