Before Markup

HALO® Module

Tissue Classifier Add-On

The Tissue Classifier Add-on utilizes a state-of-the-art machine learning algorithm to identify tissue types based on color, texture, and contextual features. Utilizing a “learn-by-example” approach, the user highlights a few distinct tissue types and within seconds the software learns to categorize tissue. The tissue classifier add-on module runs within/ is embedded in the HALO platform and can be used in conjunction with any of our cell-based analysis modules for BF or FL analysis, ultimately minimizing manual outlining of regions of interest.

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

HALO AI White Paper

Check out this white paper for an in-depth introduction to the deep learning-based add-on to HALO, including available networks, common functions, and the “train – validate – test” Validation workflow.

Fusion of Spectrally Unmixed Image Tiles into Whole Slide TIFs and HALO Image Analysis

In this application note, we describe how HALO can convert spectrally unmixed image tiles into whole slide images for analysis of the tumor microenvironment.

HALO AI High Impact Publications

Review this selection of high-impact publications for examples of HALO AI applications in fields ranging from metabolism to immuno-oncology and myology.

Quantifying Immune Cells in the Tumor Microenvironment Using HALO® Spatial Analysis Tools

In this application note, we describe two HALO analysis tools that are used to quantify the distribution of immune cells relative to tumor cells in the tumor microenvironment, Proximity Analysis and Tumor Infiltration Analysis.

Publication Spotlight

The table below includes publications that cite the Tissue Classifier 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
Understanding the impact of chemotherapy on the immune landscape of high-grade serous ovarian cancer Vanguri R, Benhamida J, Young J, Li Y, Zivanovic O, Chi D, Snyder A, Hollmann T, Mager K 2022 Gynecologic Oncology Reports Oncology Classifier, Cytonuclear, Highplex FL HALO
Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism Krstic J, Reinisch I, Schindlmaier K, Galhuber M, Riahi Z, Berger N, Kupper N, Moyschewitz E, Auer M, Michenthaler H, Nossing C, Repaoli M, Ramadani-Muja J, Usluer S, Stryeck S, Pichler M, Rinner B, Deutsch A, Reinisch A, Madl T, Chiozzi R, Heck A, Huch M, Malli R, Prokesch 2022 Science Advances Oncology Classifier HALO
Therapeutic treatment with the anti-inflammatory drug candidate MW151 may partially reduce memory impairment and normalizes hippocampal metabolic markers in a mouse model of comorbid amyloid and vascular pathology Braun D, Powell D, McLouth C, Roy S, Watterson D, Van Eldik 2022 PLOS One Neruoscience Classifier, Area Quantification HALO
A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo Kofink C, Trainor N, Mair B, Wrhrle S, Wurm M, Mischerikow N, Bader G, Rumpel K, Gerstberger T, Cui Y, Greb P, Garavel G, Scharnweber M, Fuchs J, Gremel G, Chette P, Hopf S, Budano N, Rinnenthal J, Gmaschitz G, Diers E, McLennan R, Roy M, Whitworth C, Vetma V, Mayer M, Koegl M, Ciulli A, Weinstabl H, Farnaby W 2022 Biological and Medicinal Chemistry Classifier, Cytonuclear, Multiplex IHC HALO
Pancreas resident macrophage-induced fibrosis has divergent roles in pancreas inflammatory injury and PDAC Baer J, Zuo C, Kang L, Alarcon de la Lastra A, Bocherding N, Knolhoff B, Bogner S, Zhu Y, Lewis M, Zhang N, Kim K, Fields R, Mills J, Ding L, Randolph G, DeNardo D 2022 bioRxiv Fibrosis Classifier, Area Quantification, Cytonuclear, Multiplex IHC, Highplex FL, Figure Maker HALO
Fatal Neurodissemination and SARS-CoV-2 Tropism in K18-hACE2 Mice Is Only Partially Dependent on hACE2 Expression Carossino M, Kenney D, O'Connell A, Montarnaro P, Tseng A, Gertje H, Grosz K, Ericsson M, Huber B, Kurnick S, Subramaniam S, Kirkland T, Walker J, Francis K, Klose A, Paragas N, Bosmann M, Saeed M, Balasuriya U, Douam F, Crossland N 2022 Viruses Infectious Disease Classifier, Area Quantification, Highplex FL 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
Genome-wide mapping of oncogenic pathways and genetic modifiers of chemotherapy using a high-risk hepatoblastoma genetic model Fang J, Singh S, Natarajan S, Tillman H, Abuzaid A, Durbin A, Lee H, Wu Q, Steele J, Connelly J, Cheng C, Jin H, Chen W, Fan Y, Pruett-Miller S, Rehg J, Emmons J, Cairo S, Wang R, Glazer E, Murphy A, Chen T, Davidoff A, Easton J, Chen X, Yang J 2022 Research Square Oncology Classifier HALO
Loss of ubiquitin-specific peptidase 18 destabilizes 14-3-3? protein and represses lung cancer metastasis Chen Z, Zheng L, Chen Y, Liu X, Kawakami M, Mustachi L, Roszik J, Ferry-Galow K, Parchment R, Liu X, Andresson T, Duncan G, Kurie J, Rodriguez-Canales J, Liu X, Dmitrovsky E 2022 Cancer Biology & Therapy Oncology Classifier, Cytonuclear HALO
Therapeutic impact of BET inhibitor BI 894999 treatment: backtranslation from the clinic Tontsch-Grunt U, Traexler P, Baum A, Musa H, Marzin K, Wang S, Trapani F, Engelhardt H, Solca F 2022 British Journal of Cancer Oncology Classifier, Cytonuclear, Multiplex IHC HALO
3íUTR-directed, kinase proximal mRNA decay inhibits C/EBP? phosphorylation/activation to suppress senescence in tumor cells Salotti J, Karim B, Misra S, Hu L, Basu S, Martin N, Luke B, Saylor K, Andresson T, Scheiblin D, Lockett S, Tessarollo L, Johnson P 2022 bioRxiv Oncology Classifier, Cytonuclear HALO, HALO AI
Orchestrating the Dermal/Epidermal Tissue Ratio during Wound Healing by Controlling the Moisture Content Tuca A, de Mattos I, Funk M, Winter R, Palackic A, Groeber-Becker F, Kruse D, Kukla F, Lemarchand T, Kamolz L 2022 Biomedicines Other Classifier HALO
A lncRNA signature associated with tumor immune heterogeneity predicts distant metastasis in locoregionally advanced nasopharyngeal carcinoma Liang Y, Zhang Y, Tan X, Qiao H, Liu S, Tang L, Mao Y, Chen L, Li W, Zhou G, Zhao Y, Li J, Li Q, Huang S, Gong S, Zheng Z, Li Z, Sun Y, Jiang W, Ma J, Li Y, Liu N 2022 Nature Communications Immuno-oncology Classifier, Multiplex IHC, Registration HALO
Effects of Extracorporeal Shockwave Therapy on Functional Recovery and Circulating miR-375 and miR-382-5p after Subacute and Chronic Spinal Cord Contusion Injury in Rats Ashmwe M, Posa K, Ruhrnossl A, Heinzel J, Heimel P, Mock M, Schadl B, Keibl C, Couillard-Despres S, Redl H, Mittermayr R, Hercher D 2022 Biomedicines Neuroscience, Other Classifier, Multiplex IHC HALO
The combination of gene hyperamplification and PD-L1 expression as a biomarker for the clinical benefit of tislelizumab in gastric/gastroesophageal junction adenocarcinoma Lu Z, Yang S, Luo X, Shi Y, Lee J, Deva S, Liu T, Chao Y, Zhang Y, Huang R, Xu Y, Shen Z, Shen L 2022 Gastric Cancer Immuno-oncology Classifier, Multiplex IHC HALO
Isoniazid and Rifapentine Treatment effectively reduces persistent M. tuberculosis infection 2 in macaque lungs Sharan R, Ganatra S, Singh D, Cole J, Foreman T, Thippeshappa R, Peloquin C, Shivanna V, Gonzalez O, Day C, Gandhi N, Dick E, Hall-Ursone S, Mehra S, Schlesinger L, Rengarajan J, Kaushal D 2022 Journal of Clinical Investigation Infectious Disease Classifier HALO
Prostate cancer androgen receptor activity dictates efficacy of Bipolar Androgen Therapy Sena L, Kumar R, Sanin D, Thompson E, Rosen D, Dalrymple S, Antony L, Yang Y, Comes-Alexandre C, Hicks J, Jones T, Bowers K, Eskra J, Meyers J, Gupta A, Skaist A, Yegnasubramanian S, Luo J, Brennen W, Kachhap S, Antonarakis E, De Marzo A, Isaacs J, Markowski M, Denmeade S 2022 medRxiv Oncology Classifier, Cytonuclear, Multiplex IHC, Registration HALO
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
Automated recognition of glomerular lesions in the kidneys of mice by using deep learning Akatsuka A, Horai Y, Akatsuka A 2022 Journal of Pathology Informatics Other Classifier HALO, HALO AI
MYC sensitises cells to apoptosis by driving energetic demand. Edwards-Hicks J, Su H, Mangolini M, Yoneten K, Wills J, Rodriguez-Blanco G, Young C, Cho K, Barker H, Muir M, Guerrieri A, Li X, White R, Manasterski P, Mandrou E, Wills K, Chen J, Abraham E, Sateri K, Qian B, Bankhead P, Arends M, Gammoh N, von Kriegsheim A, Patti G, Sims A, Acosta J, Brunton V, Kranc K, Christophorou M, Pearce E, Ringshausen I, Finch A 2022 Nature Communications Oncology, Metabolism Classifier HALO
Glycosphingolipids are mediators of cancer plasticity through independent signaling pathways Cumin C, Huang Y, Rossdam C, Ruoff F, Cespedes S, Liang C, Lombardo F, Coelho R, Rimmer N, Konantz M, Lopez M, Alam S, Schmidt A, Calabrese D, Fedier A, Vlajnic T, Itzstein M, Templin M, Buettner F, Everest-Dass A, Heinzelmann-Schwarz V, Jacob F 2022 Cell reports Oncology Classifier, Multiplex IHC HALO
Unveiling the tumor immune microenvironment of organ-specific melanoma metastatic sites Conway J, Rawson R, Lo S, Ahmed T, Veregara I, Gide T, Attrill G, Carlino M, Saw R, Thompson J, Spillane A, Shannon K, Shivalingam B, Menzies A, Wilmott J, Long G, Scolyer R, da Silva I 2022 Journal for ImmunoTherapy of Cancer Oncology Classifier, Spatial Analysis, Highplex FL HALO
Proliferative tumor infiltrating lymphocytes abundance within microenvironment impact clinical outcome in cutaneous B-cell lymphomas Menguy S, Prochazkova-Carolotti M, Azzi-Martin L, Ferte T, Bresson-Bepoldin L, Rey C, Vergier B, Merlio J, Beylot-Barry M, Pham-Ledard A 2022 Journal of Investigative Dermatology Immuno-oncology Classifier, Highplex FL HALO
Integrated pathological analysis to develop a Gal-9 based immune survival stratification to predict the outcome of lung large cell neuroendocrine carcinoma and its usefulness in immunotherapy Che Y, Luo Z, Cao Y, Wang J, Xue Q, Sun N, He J 2022 International Journal of Biological Sciences Oncology Classifier, Multiplex IHC HALO
PD-L1 predicts chemotherapy resistance in large-cell neuroendocrine carcinoma Che Y, Luo Z, Cao Y, Sun N, Xue Q, He J 2022 British Journal of Surgery Oncology Classifier, Multiplex IHC HALO
Systemic Nos2 Depletion and Cox inhibition limits TNBC disease progression and alters lymphoid cell spatial orientation and density Somasundaram V, Ridnour L, Cheng R, Walke A, Kedei N, Bhattacharyya D, Wink A, Edmondson E, Butcher D, Warner A, Dorsey T, Scheiblin D, Heinz W, Bryant R, Kinders R, Lipkowitz S, Wong S, Pore M, Hewitt S, McVicar D, Anderson S, Chang J, Glynn S, Ambs S, Lockett S, Wink D 2022 Redox Biology Oncology Classifer, ISH/FISH, Spatial Analysis, Registration, ISH-IHC/FISH-IF HALO
Method To Visualize the Intratumor Distribution and Impact of Gemcitabine in Pancreatic Ductal Adenocarcinoma by Multimodal Imaging Strittmatter N, Richards F, Race A, Ling S, Sutton D, Nilsson A, Wallez Y, Barnes J, Maglennon G, Gopinathan A, Brais R, Wong E, Serra M, Atkinson J, Smith A, Wilson J, Hamm G, Johnson T, Dunlop C, Kaistha B, Bunch J, Sansom O, Takats Z, Andren P, Lau A, Barry S, Goodwin R, Jodrell D 2022 Analytical Chemistry Oncology Classifier, Highplex FL HALO, HALO AI
Bone quality and composition are influenced by egg production, layer line, and estradiol-17ß in laying hens Eusemann B, Ulrich R, Sacnhez-Rodriquez E, Benavides-Reyes C, Dominguez-Gasca, Rodriguez-Navarro A, Petow S 2022 Avian Pathology Other Classifier, Multiplex IHC HALO
Tissue-resident FOLR2+ macrophages associate with CD8+ T cell infiltration in human breast cancer Ramos R, Missolo-Koussou Y, Gerber-Ferder Y, Bromley C, Bugatti M, Nunez N, Boari J, Richer W, Menger L, Denizeau J, Sedlik C, Caudana P, Kotsias F, Niborski L, Viel S, Bohec M, Lameiras S, Baulande S, Lesage L, Nicolas A, Meseure 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 2022 Cell Immuno-oncology Classifier, Spatial Analysis, Highplex FL HALO
Inflammatory Monocytes Promote Granuloma-Mediated Control of Persistent Salmonella Infection Bettke J, Tam J, Montoya V, Butler B, vander Velden A 2022 Infection and Immunity Infectious Disease Classifier, Area Quantification HALO
Reduced SARS-CoV-2 disease outcomes in Syrian hamsters receiving immune sera: Quantitative image analysis in pathologic assessments Pieda-Mora C, Robinson S, Tostanoski L, Dayao D, Chandrashekar A, Bauer K, Wrijil L, Ducat S, Hayes T, Yu J, Bondzie E, McMahan K, Sellers D, Giffin V, Hope D, Nampanya F, Mercado N, Kar S, Andersen H, Tzipori S, Barouch D, Martinot A 2022 Veterinary Pathology Infectious Disease, Other Classifier, Multiplex IHC HALO
Integrative Analysis of Bioinformatics and Machine Learning Algorithms Identifies a Novel Diagnostic Model Based on Costimulatory Molecule for Predicting Immune Microenvironment Status in Lung Adenocarcinoma Zhai W, Duan F, Wang Y, Wang J, Zhao Z, Lin Y, Rao B, Chen S, Zheng L, Long H 2022 The American Journal of Pathology Oncology Classifier, Multiplex IHC HALO
NKG2A and HLA-E define an alternative immune checkpoint axis in bladder cancer Salome B, Sfakianos J, Ranti D, Daza J, Bieber C, Charap A, Hammer C, Banchereau R, Farkas A, Ruan D, Izadmehr S, Geanon D, Kelly G, Real R, Lee B, Beaumont K, Shroff S, Wang Y, Wang Y, Thin T, Garcia-Barros M, Hegewisch-Solloa E, Mace E, Wang L, O'Donnell T, Chowell D, Fernandez-Rodriguez R, Skobe M, Taylor N, Kim-Schulze S, Sebra R, Palmer D, Clancy-Thompson E, Hammond S, Kamphorst A, Malmberg K, Marcenaro E, Romero P, Brody R, Viard M, Yuki Y, Martin M, Carrington M, Mehrazin R, Wilund P, Mellman I, Mariathasan S, Zhu J, Galsky M, Bhardwaj N, Horowitz A 2022 Cancer Cell Oncology, Immuno-oncology Classifier, Multiplex IHC HALO, HALO AI
Chronic rhinosinusitis patients display an aberrant immune cell localisation with enhanced S. aureus biofilm metabolic activity and biomass Shaghayegh G, Cooksley C, Bouras G, Panchatcharam B, Idrizi R, Jana M, Ellis S, Psaltis A, Wormald P, Vreugde S 2022 Journal of Allergy and Clinical Immunology Immunology, Infectious Disease Classifier, Spatial Analysis, Highplex FL HALO
Quantitative Dual-Energy Computed Tomography Image Guidance for Thermochemical Ablation: in vivo Results in the Rabbit VX2 Model Thompson E, Fowlkes N, Jacobsen M, Layman R, Cressman E 2022 Journal of Vascular and Interventional Radiology Oncology Classifier HALO
Innate immune receptor C5aR1 regulates cancer cell fate and can be targeted to improve radiotherapy in tumours with immunosuppressive microenvironments Beach C, MacLean D, Majorova D, Melemenidis S, Nambiar D, Kim R, Valbuena G, Guglietta S, Krieg C, Darvish D, Suwa T, Eason A, Domingo E, Moon E, Jiang D, Jiang Y, Koong A, Woodruff T, Graves E, Maughan T, Buczacki S, Stucki M, Le Q-T, Leedham S, Giaccia A, Olcina M 2023 bioRxiv Immuno-oncology Classifier, Area Quantification, Highplex FL 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
MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progression Chen J, Zheng Q, Hicks J, Trabzonlu L, Ozbek B, Jones T, Vaghasia A, Larman T, Wang R, Markowski M, Denmeade S, Pienta K, Hruban R, Antonaraskis E, Gupta A, Dang C, Yegnasubramanian S, De Marzo A 2023 bioRxiv Oncology Classifier, Area Quantification 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
Targeting XBP1 mRNA splicing sensitizes glioblastoma to chemotherapy Dowdell A, Marsland M, Faulkner S, Gedye C, Lynam J, Griffin C, Marsland J, Jiang C, Hondermarck H 2023 FASEB BioAdvances Oncology Classifier, Cytonuclear HALO
Spatial multi-omics revealed the impact of tumor ecosystem heterogeneity on immunotherapy efficacy in patients with advanced non-small cell lung cancer treated with bispecific antibody Song X, Xiong A, Wu F, Li X, Wang J, Jiang T, Chen P, Zhang X, Zhao Z, Liu H, Cheng L, Zhao C, Wang Z, Pan C, Cui X, Xu T, Luo H, Zhou C 2023 Journal for ImmunoTherapy of Cancer Immuno-oncology Classifier, Highplex FL HALO
Myeloid-specific deletion of activating transcription factor 6 alpha increases CD11b+ macrophage subpopulations and aggravates lung fibrosis Mekhael O, Revill S, Hayat A, Cass S, MacDonald K, Vierhout M, Ayoub A, Reihani A, Padwal M, Imani J, Ayaub E, Yousof T, Dvorkin-Gheva A, Rullo A, Hirota J, Richards C, Bridgewater D, Stämpfli M, Hambly N, Naqvi A, Kolb M, Ask K 2023 Immunology and Cell Biology Immunology, Fibrosis Classifier, Area Quantification, FISH, Multiplex IHC HALO
Cellular mechanisms of heterogeneity in NF2-mutant schwannoma Chiasson-MacKenzie C, Vitte J, Liu C, Wright E, Flynn E, Stott S, Giovannini M, McClatchey A 2023 Nature Communications Oncology Classifier, Multiplex IHC, Spatial Analysis, FISH-IF HALO
YBX1 integration of oncogenic PI3K/mTOR signalling regulates the fitness of malignant epithelial cells Bai Y, Gotz C, Chincarini G, Zhao Z, Slaney C, Boath J, Furic L, Angel C, Jane S, Phillips W, Stacker S, Farah C, Darido C 2023 Nature Communications Oncology Classifier, Multiplex IHC HALO
Prognostic value of tumor immune microenvironment factors in patients with stage I lung adenocarcinoma Xue Q, Wang Y, Zheng Q, Chen L, Lin Y, Jin Y, Shen X, Li Y 2023 American Journal of Cancer Research Oncology Classifier, Multiplex IHC, Highplex FL HALO
Industrialized, Artificial Intelligence-guided Laser Microdissection for Microscaled Proteomic Analysis of the Tumor Microenvironment Mitchell D, Hunt A, Conrads K, Hood B, Makohon-Moore S, Rojas C, Maxwell G, Bateman N, Conrads T 2022 JOVE Other Classifier HALO
Host, reproductive, and lifestyle factors in relation to quantitative histologic metrics of the normal breast Abubakar M, Klein A, Fan S, Lawrence S, Mutreja K, Henry J, Pfeiffer R, Duggan M, Gierach G 2023 Research Square Oncology Classifier HALO, HALO Link
Outdoor air pollution and histologic composition of normal breast tissue Ish J, Abubakar M, Fan S, Jones R, Niehoff N, Henry J, Gierach G, White A 2023 Environment International Oncology Classifier HALO
SRF617 Is a Potent Inhibitor of CD39 with Immunomodulatory and Antitumor Properties  Warren M, Matissek S, Rausch M, Panduro M, Hall R, Dulak A, Brennan D, Das Yekkirala S, Koseoglu S, Masia R, Yang Y, Reddy N, Prenovitz R, Strand J, Zaidi T, Devereaux E, Jacoberger Foissac C, Stagg J, Lee B, Holland P, Palombella V, Lake A 2023 ImmunoHorizons Immuno-oncology Classifier, Area Quantification, Multiplex IHC HALO
Sequential pembrolizumab cooperates with platinum/5FU to remodel the tumor immune microenvironment in advanced gastric cancer: A phase II chemoimmunotherapy trial Klempner S, Lee J, Mehta A, An M, Min B, Heo Y, Parikh M, Bi L, Cristescu R, Lee H, Kim T, Lee S, Moon J, Park R, Strickland M, Park W, Kang W, Kim K, Kim S 2023 Research Square Immuno-oncology Classifier, Highplex FL HALO
NLRP12-PANoptosome activates PANoptosis and pathology in response to heme and PAMPs Sundaram B, Pandian N, Mall R, Wang Y, Sarkar R, Kim H, Malireddi R, Karki R, Janke L, Vogel P, Kanneganti T 2023 Cell Immunology Classifier HALO
Epitope Lability of Phosphorylated Biomarkers of the DNA Damage Response Pathway Results in Increased Vulnerability to Effects of Delayed or Incomplete Formalin Fixation Wiseman E, Moss J, Atkinson J, Baakza H, Hayes E, Willis S, Waring P, Canales J, Jones G 2023 Journal of Histochemistry & Cytochemistry Other Classifier, Cytonuclear, Spatial Analysis HALO
Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesis Pellegrinelli V, Figueroa-Juárez E, Samuelson I, U-Din M, Rodriguez-Fdez S, Virtue S, Leggat J, Çubuk C, Peirce V, Niemi T, Campbell M, Rodriguez-Cuenca S, Dopazo Blázquez J, Carobbio S, Virtanen K, Vidal-Puig A 2023 Cell Reports Metabolism Classifier, Area Quantification, Vacuole HALO
Modifying antibody-FcRn interactions to increase the transport of antibodies through the blood-brain barrier Tien J, Leonoudakis D, Petrova R, Trinh V, Taura T, Sengupta D, Jo L, Sho A, Yun Y, Doan E, Jamin A, Hallak H, Wilson D, Stratton J 2023 mABS Neuroscience Classifier, Area Quantification, Object Colocalization HALO
The antiviral effects of a MEK1/2 inhibitor promote tumor regression in a preclinical model of human papillomavirus infection-induced tumorigenesis Luna A, Young J, Sterk R, Bondu V, Schultz F, Kusewitt D, Kang H, Ozbun M 2023 Antiviral Research Oncology, Infectious Disease Classifier, Area Quantification, Cytonuclear HALO
Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma Fang J, Singh S, Cheng C, Natarajan S, Sheppard H, Abu-Zaid A, Durbin A, Lee H, Wu Q, Steele J, Connelly J, Jin H, Chen W, Fan Y, Pruett-Miller S, Rehg J, Koo S, Santiago T, Emmons J, Cairo S, Wang R, Glazer E, Murphy A, Chen T, Davidoff A, Armengol C, Easton J, Chen X, Yang J 2023 Nature Communications Oncology Classifier HALO
Poor outcome in postpartum breast cancer patients is associated with distinct molecular and immunological features Lefrère H, Moore K, Floris G, Sanders J, Seignette I, Bismeijer T, Peters D, Broeks A, Hooijberg E, Van Calsteren K, Neven P, Warner E, Peccatori F, Loibl S, Maggen C, Han S, Jerzak K, Annibali D, Lambrechts D, de Visser K, Wessels L, Lenaerts L, Amant F 2023 Clinical Cancer Research Oncology Classifier, Highplex FL HALO, HALO AI
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
Low molecular weight heparin synergistically enhances the efficacy of adoptive and anti-PD-1-based immunotherapy by increasing lymphocyte infiltration in colorectal cancer Quan Y, He J, Zou Q, Zhang L, Sun Q, Huang H, Li W, Xie K, Wie F 2023 Journal for ImmunoTherapy of Cancer Immuno-oncology Classifier, Multiplex IHC, Highplex FL HALO
Investigating the Effects of Stereotactic Body Radiation Therapy on Pancreatic Tumor Hypoxia and Microvasculature in an Orthotopic Mouse Model using Intravital Fluorescence Microscopy Samuel T, Rapic S, Lindsay P, DaCosta RS 2023 Research Square Oncology Classifier, Area Quantification HALO
HER2-Selective and Reversible Tyrosine Kinase Inhibitor Tucatinib Potentiates the Activity of T-DM1 in Preclinical Models of HER2-positive Breast Cancer  Olson D, Taylor J, Willis K, Hensley K, Allred S, Zaval M, Farr L, Thurman R, Jain N, Hein R, Ulrich M, Peterson S, Kulukian A 2023 Cancer Research Communications Oncology Classifier, Multiplex IHC HALO
Tumor-associated macrophages trigger MAIT cell dysfunction at the HCC invasive margin Ruf B, Bruhns M, Babaei S, Kedei N, Ma L, Revsine M, Benmebarek MR, Ma C, Heinrich B, Subramanyam V, Qi J, Wabitsch S, Green BL, Bauer KC, Myojin Y, Greten LT, McCallen JD, Huang P, Trehan R, Wang X, Nur A, Soika DQM, Pouzolles M, Evans CN, Chari R, Kleiner DE, Telford W, Dadkhah K, Ruchinskas A, Stovroff MK, Kang J, Oza K, Ruchirawat M, Kroemer A, Wang XW, Claassen M, Korangy F, Greten TF 2023 Cell Immuno-oncology Classifier, Spatial Analysis, Highplex FL, Figure Maker HALO
Tumor cell HLA class I expression and pathologic response following neoadjuvant immunotherapy for newly diagnosed head and neck cancer Robbins Y, Friedman J, Redman J, Sievers C, Lassoued W, Gulley J, Allen C 2023 Oral Oncology Immuno-oncology Classifier, Spatial Analysis, Highplex FL HALO
Establishment of reference intervals of endometrial immune cells during the mid-luteal phase Yu S, Huang C, Lian R, Diao L, Zhang X, Cai S, Wei H, Chen C, Li Y, Zeng Y 2023 Journal of Reproductive Immunology Immunology Classifier, Multiplex IHC HALO
Anticoagulants Enhance Molecular and Cellular Immunotherapy of Cancer by Improving Tumor Microcirculation Structure and Function and Redistributing Tumor Infiltrates Wei F, Su Y, Quan Y, Li X, Zou Q, Zhang L, Li S, Jiang M, Lin G, Liang P, He J, Xie K 2023 Clinical Cancer Research Immuno-oncology Classifier, Multiplex IHC, Spatial Analysis, Highplex FL HALO
Apolipoprotein E induces pathogenic senescent-like myeloid cells in prostate cancer Bancaro N, Cali B, Troiani M, Elia A, Arzola R, Attanasio G, Lai P, Crespo M, Gurel B, Pereira R, Guo C, Mosole S, Brina D, D'Ambrosio M, Pasquini E, Spataro C, Zagato E, Rinaldi A, Pedotti M, Lascio S, Meani F, Montopoli M, Ferrari M, Gallina A, Varani L, Mestre R, Bolis M, Sommer S, de Bono J, Calcinotto A, Alimonti A 2023 Cancer Cell Oncology Classifier, Highplex FL HALO
Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade Pai J, Hellmann M, Sauter J, Mattar M, Rizvi H, Woo H, Shah N, Nguyen E, Uddin F, Quintanal-Villalonga A, Chan J, Manoj P, Allaj V, Baine M, Bhanot U, Jain M, Linkov I, Meng F, Brown D, Chaft J, Plodkowski A, Gigoux M, Won H, Sen T, Wells D, Donoghue M, Stanchina E, Wolchok J, Loomis B, Merghoub T, Rudin C, Chow A, Satpathy A 2023 Cancer Cell Immuno-oncology Classifier HALO
Immune profiling and RNA-seq uncover the cause of partial unexplained recurrent implantation failure Fan X, Zhao Q, Li Y, Chen Z, Liao J, Chen H, Meng F, Lu G, Lin G, Gong F 2023 International Immunopharmacology Immunology Classifier, Multiplex IHC 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
Comparing the peri-implantation endometrial T-bet/GATA3 ratio between control fertile women and patients with recurrent miscarriage: establishment and application of a reference range Get access Arrow Yu S, Diao L, Lian R, Chen C, Huang C, Li X, Li Y, Zeng Y 2023 Human Reproduction Other Classifier, Multiplex IHC HALO
Molecular determinants of clinical outcomes of pembrolizumab in recurrent ovarian cancer: Exploratory analysis of KEYNOTE-100 Ledermann JA, Shapira-Frommer R, Santin AD, Lisyanskaya AS, Pignata S, Vergote I, Raspagliesi F, Sonke GS, Birrer M, Provencher DM, Sehouli J, Colombo N, González-Martín A, Oaknin A, Ottevanger PB, Rudaitis V, Kobie J, Nebozhyn M, Edmondson M, Sun Y, Cristescu R, Jelinic P, Keefe SM, Matulonis UA 2023 Gynecologic Oncology Immuno-oncology Classifier, Highplex FL HALO
Classification of the tumor immune microenvironment and associations with outcomes in patients with metastatic melanoma treated with immunotherapies Adegoke N, Gide T, Mao Y, Quek C, Patrick E, Carlino M, Lo S, Menzies A, da Silva P, Vergara I, Long G, Scolyer R, Wilmott J 2023 Journal for ImmunoTherapy of Cancer Immuno-oncology Classifier, Highplex FL HALO
Empowering Renal Cancer Management with AI and Digital Pathology: Pathology, Diagnostics and Prognosis Ivanova E, Fayzullin A, Grinin V, Ermilov D, Arutyunyan A, Timashev P, Shekhter A 2023 Biomedicines Review Classifier, Area Quantification, Object Colocalization HALO, HALO AI
Deep radiomics-based fusion model for prediction of bevacizumab treatment response and outcome in patients with colorectal cancer liver metastases: a multicentre cohort study Zhou S, Sun D, Mao W, Liu Y, Cen W, Ye L, Liang F, Xu J, Shi H, Ji Y, Wang L, Chang W 2023 eClinicalMedicine Oncology Classifier, Multiplex IHC HALO
Unaltered hepatic wound healing response in male rats with ancestral liver injury Beil J, Perner J, Pfaller L, Gérard M, Piaia A, Doelemeyer A, Wasserkrug Naor A, Martin L, Piequet A, Dubost V, Chibout S, Moggs J, Terranova R 2023 Nature Communications Other Classifier, Area Quantification HALO, HALO AI
Disease pathology signatures in a mouse model of Mucopolysaccharidosis type IIIB Petrova R, Patil AR, Trinh V, McElroy KE, Bhakta M, Tien J, Wilson DS, Warren L, Stratton JR 2023 Scientific Reports Neuroscience, Metabolism Classifier, Area Quantification, Object Colocalization HALO
In vitro and In vivo evidence demonstrating chronic absence of Ref-1 Cysteine 65 impacts Ref-1 folding configuration, redox signaling, proliferation and metastasis in pancreatic cancer Mijit M, Kpenu E, Chowdhury N, Gampala S, Wireman R, Liu S, Babb O, Georgiadis M, Wan J, Fishel M, Kelley M 2023 Redox Biology Oncology Classifier HALO
The tumor-derived cytokine Chi3l1 induces neutrophil extracellular traps that promote T cell exclusion in triple-negative breast cancer Taifour T, Attalla SS, Zuo D, Gu Y, Sanguin-Gendreau V, Proud H, Solymoss E, Bui T, Kuasne H, Papavasiliou V, Lee CG, Kamle S, Siegel PM, Elias JA, Park M, Muller WJ 2023 Immunity Immuno-oncology Classifier, Multiplex IHC, Spatial Analysis, Highplex FL HALO
Components of the tumor immune microenvironment based on m-IHC correlate with prognosis and subtype of triple-negative breast cancer Lin L, Li H, Wang X, Wang Z, Su G, Zhou J, Sun S, Ma X, Chen Y, You C, Gu Y 2023 Cancer Medicine Immuno-oncology Classifier, Spatial Analysis, Highplex FL HALO
CD44 expression in renal tubular epithelial cells in the kidneys of rats with cyclosporine-induced chronic kidney disease Matsushita K, Toyoda T, Akane H, Morikawa T, Ogawa K 2023 Journal of Toxicologic Pathology Toxicology Classifier HALO
Integrated multi-omics profiling to dissect the spatiotemporal evolution of metastatic hepatocellular carcinoma Sun Y, Wu P, Zhang Z, Wang Z, Zhou K, Song M, Ji Y, Zang F, Lou L, Rao K, Wang P, Gu Y, Gu J, Lu B, Chen L, Pan X, Zhao X, Peng L, Liu D, Chen X, Wu K, Lin P, Wu L, Su Y, Du M, Hou Y, Yang X, Qiu S, Shi Y, Sun H, Zhou J, Huang X, Peng D, Zhang L, Fan J 2023 Cancer Cell Oncology Classifier, Multiplex IHC, Spatial Analysis, Highplex FL HALO
Tumor-associated fibrosis impairs immune surveillance and response to immune checkpoint blockade in non–small cell lung cancer Herzog B, Baer J, Borcherding N, Kingston N, Belle J, Knolhoff B, Hogg G, Ahmad F, Kang L, Petrone J, Lin C, Govindan R, Denardo D 2023 Science Translational Medicine Oncology Classifier, Multiplex IHC HALO
Analysis of several common APOBEC-type mutations in bladder tumors suggests links to viral infection  Rao N, Starrett G, Piaskowski M, Butler K, Golubeva Y, Yan W, Lawrence S, Dean M, Garcia-Closas M, Baris D, Johnson A, Schwenn M, Malats N, Real F, Kogevinas M, Rothman N, Silverman D, Dyrskjøt L, Buck C, Koutros S, Prokunina-Olsson L 2023 Cancer Prevention Research Oncology Classifier, Immune HALO
Complex Urban Atmospheres alters Alveolar Stem Cells Niche Properties and drives Lung Fibrosis Belgacemi R, Baptista BR, Justeau G, Toigo M, Frauenpreis A, Yilmaz R, Der Vartanian A, Cazaunau M, Pangui E, Bergé A, Gratien A, Macias Rodriguez JC, Bellusci S, Derumeaux G, Boczkowski J, Al Alam D, Coll P, Lanone S, Boyer L 2023 American Journal of Physiology - Lung Cellular and Molecular Physiology Fibrosis Classifier, Area Quantification, Highplex FL HALO
The tumor microenvironment state associates with response to HPV therapeutic vaccination in patients with respiratory papillomatosis NORBERG S, BAI K, SIEVERS C, ROBBINS Y, FRIEDMAN J, YANG X, KENYON M, WARD E, SCHLOM J, GULLEY J, LANKFORD A, SEMNANI R, SABZEVARI H, BROUGH D, ALLEN C 2023 Science Translational Medicine Oncology Classifier, Highplex FL HALO, HALO AI
Role of CD44 expressed in renal tubules during maladaptive repair in renal fibrogenesis in an allopurinol-induced rat model of chronic kidney disease Matsushita K, Toyoda T, Akane H, Morikawa T, Ogawa K 2023 Journal of Applied Toxicology Toxicology Classifier HALO
Exocrine pancreas in type 1 and type 2 diabetes: different patterns of fibrosis, metaplasia, angiopathy, and adiposity  Wright J, Eskaros A, Windon A, Bottino R, Jenkins R, Bradley A, Aramandla R, Philips S, Kang H, Saunders D, Brissova M, Powers A 2023 Diabetes Gastroenterology Classifier, Highplex FL HALO
A modified mouse model of Friedreich's ataxia with conditional Fxn allele homozygosity delays onset of cardiomyopathy Perfitt TL, Huichalaf C, Gooch R, Kuperman A, Ahn Y, Chen X, Ullas S, Hirenallur-Shanthappa D, Zhan Y, Otis D, Whiteley LO, Bulawa C, Martelli A 2023 American Journal of Physiology-Heart and Circulatory Physiology Other Classifier, Area Quantification HALO

Related HALO Modules

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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Spatial Analysis

Plot cells and objects from one or more images and perform nearest neighbor analysis, proximity analysis, and tumor infiltration analysis.

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