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
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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