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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!

Title Authors Year Journal Application HALO Modules Product
Kaiso (ZBTB33) subcellular partitioning functionally links LC3A/B, the tumor microenvironment, and breast cancer survival Singhal SK, Byun JS, Park S, Yan T, Yancey R, Caban A, Hernandez SG, Hewitt SM, Boisvert H, Hennek S, Bobrow M, Ahmed SU, White J, Yates C, Aukerman A, Vanguri R, Bareja R, Lenci R, FarrÈ PL, De Siervi A, N·poles AM, Vohra N, Gardner K 2021 Communications Biology Oncology Cytonuclear, TMA HALO
The prevalence and prognostic significance of estrogen receptor beta expression in non-small cell lung cancer Enwere EK, Dean ML, Li H, D'Silva A, Bebb DG 2020 Translational Lung Cancer Research Oncology Cytonuclear, TMA HALO
Prevalence of CD8+ cytotoxic lymphocytes in human neoplasms Blessin NC, Spriestersbach P, Li W, Mandelkow T, Dum D, Simon R, Hube-Magg C, Lutz F, Viehweger F, Lennartz M, Fraune C, Nickelsen V, Fehrle W, Gˆbel C, Weidemann S, Clauditz T, Lebok P, Mˆller K, Steurer S, Izbicki JR, Sauter G, Minner S, Jacobsen F, Luebke AM, B¸scheck F, Hˆflmayer D, Wilczak W, Burandt E, Hinsch A 2020 Cellular Oncology Oncology, Immuno-oncology Membrane, TMA HALO
Mechanical regulation of glycolysis via cytoskeleton architecture Park JS, Burckhardt CJ, Lazcano R, Solis LM, Isogai T, Li L, Chen CS, Gao B, Minna JD, Bachoo R, DeBerardinis RJ, Danuser G 2020 Nature Oncology Classifier, Cytonuclear, TMA HALO
Prognostic significance of mesothelin expression in colorectal cancer disclosed by area-specific four-point tissue microarrays Shiraishi T, Shinto E, Nearchou IP, Tsuda H, Kajiwara Y, Einama T, Caie PD, Kishi Y, Ueno H 2020 Vichows Archiv Oncology Cytonuclear, TMA HALO AI
Prognostic and Predictive Value of Tumor-infiltrating Leukocytes and of Immune Checkpoint Molecules PD1 and PDL1 in Clear Cell Renal Cell Carcinoma Stenzel PJ, Schindeldecker M, Teagscherer KE, Foersch S, Herpel E, Hohenfellner M, Hatiboglu G, Alt J, Thomas C, Haferkamp A, Roth W, Macher-Goeppinger S 2020 Translational Oncology Oncology, Immuno-oncology Classifier, Cytonuclear, TMA HALO
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
Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis Czauderna C, Poplawski A, O'Roourke C, Castven D, PÈrez-Aguilar B, Becker D, Heilmann-Heimbach S, Odenthal M, Amer W, Schmiel M, Drebber U, Binder H, Ridder D, Schindeldecker M, Straub B, Galle P, Andersen J, Thorgeirsson S, Park Y, Marquardt J 2021 JCI Insight Oncology Cytonuclear, TMA HALO
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
B7-H3 immune checkpoint expression is a poor prognostic factor in colorectal carcinoma Lu Z, Zhao Z-X, Cheng P, Huang F, Guan X, Zhang M-G, Chen H-P, Liu Z, Jiang Z, Zheng Z-X, Zou S-M, Wang X-S 2020 Modern Pathology Immuno-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
PLX3397 treatment inhibits constitutive CSF1R-induced oncogenic ERK signaling, reduces tumor growth, and metastatic burden in osteosarcoma Smeester BA, Slipek NJ, Pomeroy EJ, Laoharawee K, Osum SH, Larsson AT, Williams KB, Stratton N, Yamamoto K, Peterson JJ, Rathe SK, Mills LJ, Hudson WA, Crosby MR, Wang M, Rahramann EP, Moriarity SB, Largaespada DA 2020 Bone Oncology Cytonuclear, TMA HALO
Diagnostic and prognostic implications of a three-antibody molecular subtyping algorithm for non-muscle invasive bladder cancer Jackson C, Chen L, Hardy C, Ren K, Visram K, Bratti V, Johnstone J, SjÀÜdahl G, Siemens D, Gooding R, Berman D 2021 The Journal of Pathology: Clinical Research Oncology Cytonuclear, TMA HALO
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
Comprehensive clinicopathologic study of alpha fetoprotein-expression in a large cohort of patients with hepatocellular carcinoma Ridder D, Weinmann A, Schindeldecker M, Urbansky L, Berndt K, Gerber T, Lang H, Lotz J, Lackner K, Roth W, Straub B 2021 International Journal of Cancer Oncology Cytonuclear, 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
Comparing Deep Learning and Immunohistochemistry in Determining the Site of Origin for Well-Differentiated Neuroendocrine Tumors Redemann J, Schultz F, Martinez C, Harrell M, Clark D, Martin D, Hanson J 2020 Journal of Pathology Informatics Oncology Cytonuclear, 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

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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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