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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)
  • KFBIO (KFB, KFBF)
  • DICOM (DCM*)
    *whole-slide images

Lunaphore COMET Hyperplex IF and HALO® Image Analysis eBook

Our collaborative eBook with Lunaphore shows how HALO and HALO AI, alongside the Lunaphore COMET instrument, enable a high-throughput workflow for phenotypic and spatial analysis of cells in the tumor microenvironment.

Spatial Characterization of the TME with Cell DIVE Multiplexed Imaging and HALO Image Analysis

Check out our collaborative poster with Cell Signaling Technology and Leica Microsystems to learn about a combined workflow for spatial analysis of the TME.

Clustering Workflow for Advanced Cell Phenotyping of Hyperplex IF Images

Download our collaborative poster with Lunaphore to learn about a clustering workflow that uses unsupervised learning for COMET™ images.

Lunaphore COMET Hyperplex IF and HALO® Image Analysis of the TME

Download our collaborative poster with Lunaphore to see how HALO and HALO AI, alongside the Lunaphore COMET instrument, enable a high throughput workflow for phenotypic and spatial analysis of cells in the tumor microenvironment.

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.

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!

Title Authors Year Journal Application HALO Modules Product
Linking epigenetic signature and metabolic phenotype in IDH mutant and IDH wildtype diffuse glioma Buran 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 PN 2020 Neuropathology and Applied Neurobiology Neuroscience Multiplex IHC, TMA HALO
The role of WNT10B in normal prostate gland development and prostate cancer Madueke I, Hu W-Y, Hu D, Swanson SM, Griend DV, Abern M, Prins GS 2019 The Prostate Oncology Multiplex IHC, TMA HALO
Tumor cell PD-L1 expression is a strong predictor of unfavorable prognosis in immune checkpoint therapy-naive clear cell renal cell cancer Mˆller 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 TS 2021 International Urology and Nephrology Immuno-oncology Multiplex IHC, TMA HALO
Prognostic role of proliferating CD8+ cytotoxic Tcells in human cancers Blessin 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 S 2021 Cellular Oncology Immuno-oncology Highplex FL, TMA HALO
Tertiary lymphoid structures critical for prognosis in endometrial cancer patients - a TransPORTEC study Horeweg 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 M 2021 Research Square Multiplex IHC, TMA HALO AI
Genomic analysis of Vascular Invasion in Hepatocellular Carcinoma (HCC) Reveals Molecular Drivers and Predictive Biomarkers Krishnan 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 R 2020 Hepatology Oncology Multiplex IHC, TMA HALO
T-regulatory cells predict clinical outcome in soft tissue sarcoma patients: a clinico-pathological study Smolle 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 J 2021 British Journal of Cancer Oncology Highplex FL, TMA HALO
PIK3CA mutation and CNV status and post-chemoradiotherapy survival in patients with cervical cancer Martell K, McIntyre JB, Kornaga EN, Chan AMY, Phan T, Kobel M, Enwere EK, Dean ML, Ghatage P, Lees-Miller SP, Doll CM 2020 Gynecologic Oncology Oncology Classifier, Highplex FL, TMA HAO
Tissue-resident FOLR2+ macrophages associate with tumor-infiltrating CD8+ T cells and with increased survival of breast cancer patients Ramos, 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 J 2021 bioRxiv Immuno-oncology Cytonuclear, Highplex FL, TMA HALO
Nuclear expression of pSTAT3Tyr705†and pSTAT3Ser727†in the stromal compartment of localized hormone-naÔve prostate cancer Marginean F, Hellsten R, Krzyanowska A, Bjartell A 2022 Pathology - Research and Practice Oncology Cytonuclear, Multiplex IHC, TMA HALO
Tertiary lymphoid structures critical for prognosis in endometrial cancer patients - a TransPORTEC study Horeweg 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 M 2022 Nature Communications Oncology Cytonuclear, Multiplex IHC, TMA HALO, HALO AI
Genomic and single-cell landscape reveals novel drivers and therapeutic vulnerabilities of transformed cutaneous T-cell lymphoma Song 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 P 2022 Cancer Discovery Oncology Cytonuclear, Highplex FL, TMA HALO
Multiplex Immunohistochemical Phenotyping of T Cells in Primary Prostate Cancer Ozbek B, Ertunc O, Erickson A, Vidal I, Gomes-Alexandre C, Guner G, Hicks J, Jones T, Taube J, Sfanos K, Yegnasubramanian S, DeMarzo A 2022 The Prostate Immuno-oncology Classifier, Cytonuclear, Highplex FL, Serial Section, Registration, Figure Maker, TMA HALO
SPOP promotes cervical cancer progress by inducing PD-1 move away from PD-L1 in spatial localization Wu J, Wu Y, Guo Q, Chen S, Wang S, Zhu J, Wu X, Ju X 2022 Research Square Oncology Cytonuclear, Spatial Analysis, Highplex FL, TMA HALO
Type I interferon regulates proteolysis by macrophages to prevent immunopathology following viral infection Lee 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 A 2022 PLOS Pathogens Infectious Disease Area Quantification, Multiplex IHC, TMA HALO
Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer Horeweg 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 D 2020 Cancer Immunology Research Oncology Cytonuclear, Multiplex IHC, TMA HALO, HALO AI
Prognostic image-based quantification of CD8CD103 T cell subsets in high-grade serous ovarian cancer patients Paijens 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 H 2021 OncoImmunology Immuno-oncology Cytonuclear, Multiplex IHC, TMA HALO, HALO AI
Senescence-Associated Molecules and Tumor-Immune-Interactions as Prognostic Biomarkers in Colorectal Cancer Kellers F, Fernandez A, Konykiewitz B, Schindeldecker M, Tagscherer K, Heintz A, Jesinghaus M, Roth W, Foersch S 2022 Frontiers in Medicine Oncology Classifier, Multiplex IHC, Spatial Analysis, Registration, TMA HALO
A survey on artificial intelligence in histopathology image analysis Abdelsamea M, Zidan U, Senousy Z, Gaber M, Rakha E, Ilyas M 2022 WIREs Data Mining and Knowledge Discovery Review Classifier, Cytonuclear, Figure Maker, TMA HALO
LncRNA scaRNA2 bridges DNA end-resection to homologous recombination repair mediated chemoradioresistance Yang 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 F 2022 Research Square Oncology Highplex FL, TMA HALO
The proteomic landscape of glioblastoma recurrence reveals novel and targetable immunoregulatory drivers Tatari 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 P 2022 Acta Neuropathologica Oncology Multiplex IHC, Figure Maker, TMA HALO
The MK2/Hsp27 axis is a major survival mechanism for pancreatic ductal adenocarcinoma under genotoxic stress Grierson P, Dodhiawala P, Cheng Y, Chen T, Khawar I, Wei Q, Zhang D, Li L, Herndon J, Monahan J, Ruzinova M, Lim K 2021 Science Translational Medicine Oncology Area Quantification, TMA HALO
SIGLEC15 amplifies immunosuppressive properties of tumor-associated macrophages in pancreatic cancer Li, 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 W 2022 Cancer Letters Immuno-oncology Highplex FL, TMA HALO
Developing a Nomogram for Preoperative Prediction of Cervical Cancer Lymph Node Metastasis by Multiplex Immunofluorescence Wu J, Guo Q, Zhu J, Wu Y, Liang S Chen S, Wang S, Ju X, Wu X 2022 Authorea Oncology Spatial Analysis, Highplex FL, TMA HALO
AKR1C3 regulated by NRF2/MAFG complex promotes proliferation via stabilizing PARP1 in hepatocellular carcinoma Pan 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 L 2022 Oncogene Oncology Area Quantification, TMA HALO
The chromatin remodeler CHD6 promotes colorectal cancer development by regulating TMEM65-mediated mitochondrial dynamics via EGF and Wnt signaling Zhang 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 M 2022 Cell Discovery Oncology Multiplex IHC, TMA HALO
Low CD8 T Cell Counts Predict Benefit from Hypoxia-Modifying Therapy in Muscle-Invasive Bladder Cancer Smith V, Mukherjee D, Tsakiroglou A, Baker A, Mistry H, Choudhury A, Hoskin P, Illidge T, West C 2022 Cancers Immuno-oncology Highplex FL, TMA HALO
NADK-mediated de novo NADP(H) synthesis is a metabolic adaptation essential for breast cancer metastasis Ilter D, Drapela S, Schild T, Ward N, Adhikari E, Low V, Asara J, Oskarsson T, Lau E, DeNicola G, McReynolds M, Gomes A 2023 Redox Biology Oncology, Metabolism Classifier, Highplex FL, TMA HALO
PD-1+CD8+ T Cells Proximal to PD-L1+CD68+ Macrophages Are Associated with Poor Prognosis in Pancreatic Ductal Adenocarcinoma Patients Yang X, Wang G, Song Y, Zhuang T, Li Y, Xie Y, Fei X, Zhao Y, Xu D, Hu Y 2023 Cancers Oncology, Immuno-oncology Classifier, Spatial Analysis, Highplex FL, Registration, TMA HALO
Differential expression of CD8 defines phenotypically distinct cytotoxic T cells in cancer and multiple sclerosis Burkard T, Herrero San Juan M, Dreis C, Kiprina A, Namgaladze D, Siebenbrodt K, Luger S, Foerch C, Pfeilschifter J, Weigert A, Radeke H 2023 Clinical and Translational Medicine Oncology, immunology Classifier, Spatial Analysis, Highplex FL, TMA HALO
The CD73 is induced by TGF-β1 triggered by nutrient deprivation and highly expressed in dedifferentiated human melanoma Giraulo C, Turiello R, Orlando L, Leonardelli S, Landsberg J, Belvedere R, Rolshoven G, Muller C, Holzel M, Morello S 2023 Biomedicine & Pharmacotherapy Oncology Highplex FL, TMA HALO, HALO AI
ATR-binding lncRNA ScaRNA2 promotes cancer resistance through facilitating efficient DNA end resection during homologous recombination repair Chen 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 Y 2023 Journal of Experimental & Clinical Cancer Research Oncology Highplex FL, TMA HALO
Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability Benabdallah 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 A 2023 Nature Structural & Molecular Biology Oncology Multiplex IHC, TMA HALO, HALO AI
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
Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression Macke 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 A 2023 Molecular Cancer Research Oncology Classifier, Area Quantification, Multiplex IHC, TMA HALO
FSCN1 and epithelial mesenchymal transformation transcription factor expression in human pancreatic intraepithelial neoplasia and ductal adenocarcinoma Morris HT, Bamlet WR, Razidlo GL, Machesky LM 2023 Pathology - Research and Practice Oncology Cytonuclear, TMA HALO
Positive regulatory loop of platelet-derived growth factor DD-induced STAT3 activation is associated with poor prognosis in advanced urothelial carcinoma Ando K, Kurashina R, Motoi N, Iizuka T, Inoue M, Maruyama R, Mitani K, Takenobu H, Haruta M, Onuki R, Matsuoka Y, Kamijo T, Kageyama Y 2023 Biochemical and Biophysical Research Communications Oncology Multiplex IHC, TMA HALO
A neutrophil extracellular traps-related classification predicts prognosis and response to immunotherapy in colon cancer Feng C, Li Y, Tai Y, Zhang W, Wang H, Lian S, Jin-si-han E, Liu Y, Li X, Chen Q, He M, Lu Z 2023 Scientific Reports Immuno-oncology Spatial Analysis, Highplex FL, Figure Maker, TMA HALO
CD15 Is a Risk Predictor and a Novel Target in Clear Cell Renal Cell Carcinoma Stenzela PJ, Schindeldeckera MS, Seidmanna L, Herpel E, Hohenfellnere M, Hatiboglue G, Foerscha S, Porubskya S, Macher-Goeppingera S, Rotha W, Tagscherer KE 2023 Pathobiology Oncology Multiplex IHC, TMA HALO
ERBB3 overexpression is enriched in diverse patient populations with castration-sensitive prostate cancer and is associated with a unique AR activity signature Vellky J E, Kirkpatrick B J, Gutgesell L C, Morales M, Brown R M, Wu Y, Maienschein-Cline M, Notardonato L D, Weinfeld M S, Nguyen R H, Brister E, Sverdlov M, Liu L, Xu Z, Kregel S, Nonn L, Vander Griend D J, Reizine N M 2024 Clinical Cancer Research Oncology Area Quantification, TMA HALO, HALO AI
Multiplex analysis of intratumoural immune infiltrate and prognosis in patients with stage II–III colorectal cancer from the SCOT and QUASAR 2 trials: a retrospective analysis Frei AL, McGuigan A, Sinha RAK, Jabbar F, Gneo L, Tomasevic T, Harkin A, Iveson T, Saunders MP, Oien KA, Maka N, Pezzella F, Campo L, Browne M, Glaire M, Kildal W, Danielsen HE, Hay J, Edwards J, Sansom O, Kelly C, Tomlinson I, Kerr R, Kerr D, Domingo E, consortium T, Church DN, Koelzer VH 2024 The Lancet Oncology Immuno-oncology Area Quantification, Highplex FL, TMA HALO, HALO AI
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
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

Related HALO Modules

Multiplex IHC

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

Learn More
Highplex FL

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

Learn More
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.

Learn More

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