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)
  • DICOM (DCM*)
    *whole-slide images

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.

Spatial Analysis Application Note

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

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.

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.

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 Tissue Classifier Add-on. 

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

TitleAuthorsYearJournalApplicationHALO ModulesProduct
Understanding the impact of chemotherapy on the immune landscape of high-grade serous ovarian cancerVanguri R, Benhamida J, Young J, Li Y, Zivanovic O, Chi D, Snyder A, Hollmann T, Mager K2022Gynecologic Oncology ReportsOncologyClassifier, Cytonuclear, Highplex FLHALO
Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergismKrstic 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, Prokesch2022Science AdvancesOncologyClassifierHALO
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 pathologyBraun D, Powell D, McLouth C, Roy S, Watterson D, Van Eldik2022PLOS OneNeruoscienceClassifier, Area QuantificationHALO
A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivoKofink 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 W2022Biological and Medicinal ChemistryClassifier, Cytonuclear, Multiplex IHCHALO
Pancreas resident macrophage-induced fibrosis has divergent roles in pancreas inflammatory injury and PDACBaer 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 D2022bioRxivFibrosisClassifier, Area Quantification, Cytonuclear, Multiplex IHC, Highplex FL, Figure MakerHALO
Fatal Neurodissemination and SARS-CoV-2 Tropism in K18-hACE2 Mice Is Only Partially Dependent on hACE2 ExpressionCarossino 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 N2022VirusesInfectious DiseaseClassifier, Area Quantification, Highplex FLHALO
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
Genome-wide mapping of oncogenic pathways and genetic modifiers of chemotherapy using a high-risk hepatoblastoma genetic modelFang 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 J2022Research SquareOncologyClassifierHALO
Loss of ubiquitin-specific peptidase 18 destabilizes 14-3-3? protein and represses lung cancer metastasisChen 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 E2022Cancer Biology & TherapyOncologyClassifier, CytonuclearHALO
Therapeutic impact of BET inhibitor BI 894999 treatment: backtranslation from the clinicTontsch-Grunt U, Traexler P, Baum A, Musa H, Marzin K, Wang S, Trapani F, Engelhardt H, Solca F2022British Journal of CancerOncologyClassifier, Cytonuclear, Multiplex IHCHALO
3íUTR-directed, kinase proximal mRNA decay inhibits C/EBP? phosphorylation/activation to suppress senescence in tumor cellsSalotti J, Karim B, Misra S, Hu L, Basu S, Martin N, Luke B, Saylor K, Andresson T, Scheiblin D, Lockett S, Tessarollo L, Johnson P2022bioRxivOncologyClassifier, CytonuclearHALO, HALO AI
Orchestrating the Dermal/Epidermal Tissue Ratio during Wound Healing by Controlling the Moisture ContentTuca A, de Mattos I, Funk M, Winter R, Palackic A, Groeber-Becker F, Kruse D, Kukla F, Lemarchand T, Kamolz L2022BiomedicinesOtherClassifierHALO
A lncRNA signature associated with tumor immune heterogeneity predicts distant metastasis in locoregionally advanced nasopharyngeal carcinomaLiang 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 N2022Nature CommunicationsImmuno-oncologyClassifier, Multiplex IHC, RegistrationHALO
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 RatsAshmwe M, Posa K, Ruhrnossl A, Heinzel J, Heimel P, Mock M, Schadl B, Keibl C, Couillard-Despres S, Redl H, Mittermayr R, Hercher D2022BiomedicinesNeuroscience, OtherClassifier, Multiplex IHCHALO
The combination of gene hyperamplification and PD-L1 expression as a biomarker for the clinical benefit of tislelizumab in gastric/gastroesophageal junction adenocarcinomaLu Z, Yang S, Luo X, Shi Y, Lee J, Deva S, Liu T, Chao Y, Zhang Y, Huang R, Xu Y, Shen Z, Shen L2022Gastric CancerImmuno-oncologyClassifier, Multiplex IHCHALO
Isoniazid and Rifapentine Treatment effectively reduces persistent M. tuberculosis infection 2 in macaque lungsSharan 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 D2022Journal of Clinical InvestigationInfectious DiseaseClassifierHALO
Prostate cancer androgen receptor activity dictates efficacy of Bipolar Androgen TherapySena 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 S2022medRxivOncologyClassifier, Cytonuclear, Multiplex IHC, RegistrationHALO
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
Automated recognition of glomerular lesions in the kidneys of mice by using deep learningAkatsuka A, Horai Y, Akatsuka A2022Journal of Pathology InformaticsOtherClassifierHALO, 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 A2022Nature CommunicationsOncology, MetabolismClassifierHALO
Glycosphingolipids are mediators of cancer plasticity through independent signaling pathwaysCumin 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 F2022Cell reportsOncologyClassifier, Multiplex IHCHALO
Unveiling the tumor immune microenvironment of organ-specific melanoma metastatic sitesConway 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 2022Journal for ImmunoTherapy of CancerOncologyClassifier, Spatial Analysis, Highplex FLHALO
Proliferative tumor infiltrating lymphocytes abundance within microenvironment impact clinical outcome in cutaneous B-cell lymphomasMenguy S, Prochazkova-Carolotti M, Azzi-Martin L, Ferte T, Bresson-Bepoldin L, Rey C, Vergier B, Merlio J, Beylot-Barry M, Pham-Ledard A2022Journal of Investigative DermatologyImmuno-oncologyClassifier, Highplex FLHALO
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 immunotherapyChe Y, Luo Z, Cao Y, Wang J, Xue Q, Sun N, He J2022International Journal of Biological SciencesOncologyClassifier, Multiplex IHCHALO
PD-L1 predicts chemotherapy resistance in large-cell neuroendocrine carcinomaChe Y, Luo Z, Cao Y, Sun N, Xue Q, He J2022British Journal of SurgeryOncologyClassifier, Multiplex IHCHALO
Systemic Nos2 Depletion and Cox inhibition limits TNBC disease progression and alters lymphoid cell spatial orientation and densitySomasundaram 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 D2022Redox BiologyOncologyClassifer, ISH/FISH, Spatial Analysis, Registration, ISH-IHC/FISH-IFHALO
Method To Visualize the Intratumor Distribution and Impact of Gemcitabine in Pancreatic Ductal Adenocarcinoma by Multimodal ImagingStrittmatter 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 D2022Analytical ChemistryOncologyClassifier, Highplex FLHALO, HALO AI
Bone quality and composition are influenced by egg production, layer line, and estradiol-17ß in laying hensEusemann B, Ulrich R, Sacnhez-Rodriquez E, Benavides-Reyes C, Dominguez-Gasca, Rodriguez-Navarro A, Petow S2022Avian PathologyOtherClassifier, Multiplex IHCHALO
Tissue-resident FOLR2+ macrophages associate with CD8+ T cell infiltration in human breast cancerRamos 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 J2022CellImmuno-oncologyClassifier, Spatial Analysis, Highplex FLHALO
Inflammatory Monocytes Promote Granuloma-Mediated Control of Persistent Salmonella InfectionBettke J, Tam J, Montoya V, Butler B, vander Velden A2022Infection and ImmunityInfectious DiseaseClassifier, Area QuantificationHALO
Reduced SARS-CoV-2 disease outcomes in Syrian hamsters receiving immune sera: Quantitative image analysis in pathologic assessmentsPieda-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 A2022Veterinary PathologyInfectious Disease, OtherClassifier, Multiplex IHCHALO
Integrative Analysis of Bioinformatics and Machine Learning Algorithms Identifies a Novel Diagnostic Model Based on Costimulatory Molecule for Predicting Immune Microenvironment Status in Lung AdenocarcinomaZhai W, Duan F, Wang Y, Wang J, Zhao Z, Lin Y, Rao B, Chen S, Zheng L, Long H2022The American Journal of PathologyOncologyClassifier, Multiplex IHCHALO
NKG2A and HLA-E define an alternative immune checkpoint axis in bladder cancerSalome 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 A2022Cancer CellOncology, Immuno-oncologyClassifier, Multiplex IHCHALO, HALO AI
Chronic rhinosinusitis patients display an aberrant immune cell localisation with enhanced S. aureus biofilm metabolic activity and biomassShaghayegh G, Cooksley C, Bouras G, Panchatcharam B, Idrizi R, Jana M, Ellis S, Psaltis A, Wormald P, Vreugde S2022Journal of Allergy and Clinical ImmunologyImmunology, Infectious DiseaseClassifier, Spatial Analysis, Highplex FLHALO
Quantitative Dual-Energy Computed Tomography Image Guidance for Thermochemical Ablation: in vivo Results in the Rabbit VX2 ModelThompson E, Fowlkes N, Jacobsen M, Layman R, Cressman E2022Journal of Vascular and Interventional RadiologyOncologyClassifierHALO
Innate immune receptor C5aR1 regulates cancer cell fate and can be targeted to improve radiotherapy in tumours with immunosuppressive microenvironmentsBeach 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 M2023bioRxivImmuno-oncologyClassifier, Area Quantification, Highplex FLHALO
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
MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progressionChen 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 A2023bioRxivOncologyClassifier, Area QuantificationHALO
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
Targeting XBP1 mRNA splicing sensitizes glioblastoma to chemotherapyDowdell A, Marsland M, Faulkner S, Gedye C, Lynam J, Griffin C, Marsland J, Jiang C, Hondermarck H2023FASEB BioAdvancesOncologyClassifier, CytonuclearHALO
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 C2023Journal for ImmunoTherapy of CancerImmuno-oncologyClassifier, Highplex FLHALO
Myeloid-specific deletion of activating transcription factor 6 alpha increases CD11b+ macrophage subpopulations and aggravates lung fibrosisMekhael 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 K2023Immunology and Cell BiologyImmunology, FibrosisClassifier, Area Quantification, FISH, Multiplex IHCHALO
Cellular mechanisms of heterogeneity in NF2-mutant schwannomaChiasson-MacKenzie C, Vitte J, Liu C, Wright E, Flynn E, Stott S, Giovannini M, McClatchey A2023Nature CommunicationsOncologyClassifier, Multiplex IHC, Spatial Analysis, FISH-IFHALO
YBX1 integration of oncogenic PI3K/mTOR signalling regulates the fitness of malignant epithelial cellsBai Y, Gotz C, Chincarini G, Zhao Z, Slaney C, Boath J, Furic L, Angel C, Jane S, Phillips W, Stacker S, Farah C, Darido C2023Nature CommunicationsOncologyClassifier, Multiplex IHCHALO
Prognostic value of tumor immune microenvironment factors in patients with stage I lung adenocarcinomaXue Q, Wang Y, Zheng Q, Chen L, Lin Y, Jin Y, Shen X, Li Y2023American Journal of Cancer ResearchOncologyClassifier, Multiplex IHC, Highplex FLHALO
Industrialized, Artificial Intelligence-guided Laser Microdissection for Microscaled Proteomic Analysis of the Tumor MicroenvironmentMitchell D, Hunt A, Conrads K, Hood B, Makohon-Moore S, Rojas C, Maxwell G, Bateman N, Conrads T2022JOVEOtherClassifierHALO
Host, reproductive, and lifestyle factors in relation to quantitative histologic metrics of the normal breastAbubakar M, Klein A, Fan S, Lawrence S, Mutreja K, Henry J, Pfeiffer R, Duggan M, Gierach G2023Research SquareOncologyClassifierHALO, HALO Link
Outdoor air pollution and histologic composition of normal breast tissueIsh J, Abubakar M, Fan S, Jones R, Niehoff N, Henry J, Gierach G, White A2023Environment InternationalOncologyClassifierHALO
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 A2023ImmunoHorizonsImmuno-oncologyClassifier, Area Quantification, Multiplex IHCHALO
Sequential pembrolizumab cooperates with platinum/5FU to remodel the tumor immune microenvironment in advanced gastric cancer: A phase II chemoimmunotherapy trialKlempner 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 S2023Research SquareImmuno-oncologyClassifier, Highplex FLHALO
NLRP12-PANoptosome activates PANoptosis and pathology in response to heme and PAMPsSundaram B, Pandian N, Mall R, Wang Y, Sarkar R, Kim H, Malireddi R, Karki R, Janke L, Vogel P, Kanneganti T2023CellImmunologyClassifierHALO
Epitope Lability of Phosphorylated Biomarkers of the DNA Damage Response Pathway Results in Increased Vulnerability to Effects of Delayed or Incomplete Formalin FixationWiseman E, Moss J, Atkinson J, Baakza H, Hayes E, Willis S, Waring P, Canales J, Jones G2023Journal of Histochemistry & CytochemistryOtherClassifier, Cytonuclear, Spatial AnalysisHALO
Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesisPellegrinelli 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 A2023Cell ReportsMetabolismClassifier, Area Quantification, VacuoleHALO
Modifying antibody-FcRn interactions to increase the transport of antibodies through the blood-brain barrierTien 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 J2023mABSNeuroscienceClassifier, Area Quantification, Object ColocalizationHALO
The antiviral effects of a MEK1/2 inhibitor promote tumor regression in a preclinical model of human papillomavirus infection-induced tumorigenesisLuna A, Young J, Sterk R, Bondu V, Schultz F, Kusewitt D, Kang H, Ozbun M2023Antiviral ResearchOncology, Infectious DiseaseClassifier, Area Quantification, CytonuclearHALO
Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastomaFang 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 J2023Nature CommunicationsOncologyClassifierHALO
Poor outcome in postpartum breast cancer patients is associated with distinct molecular and immunological featuresLefrère 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 F2023Clinical Cancer ResearchOncologyClassifier, Highplex FLHALO, HALO AI
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
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 F2023Journal for ImmunoTherapy of CancerImmuno-oncologyClassifier, Multiplex IHC, Highplex FLHALO
Investigating the Effects of Stereotactic Body Radiation Therapy on Pancreatic Tumor Hypoxia and Microvasculature in an Orthotopic Mouse Model using Intravital Fluorescence MicroscopySamuel T, Rapic S, Lindsay P, DaCosta RS2023Research SquareOncologyClassifier, Area QuantificationHALO
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 A2023Cancer Research CommunicationsOncologyClassifier, Multiplex IHCHALO
Tumor-associated macrophages trigger MAIT cell dysfunction at the HCC invasive marginRuf 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 TF2023CellImmuno-oncologyClassifier, Spatial Analysis, Highplex FL, Figure MakerHALO
Tumor cell HLA class I expression and pathologic response following neoadjuvant immunotherapy for newly diagnosed head and neck cancerRobbins Y, Friedman J, Redman J, Sievers C, Lassoued W, Gulley J, Allen C2023Oral OncologyImmuno-oncologyClassifier, Spatial Analysis, Highplex FLHALO
Establishment of reference intervals of endometrial immune cells during the mid-luteal phaseYu S, Huang C, Lian R, Diao L, Zhang X, Cai S, Wei H, Chen C, Li Y, Zeng Y2023Journal of Reproductive ImmunologyImmunologyClassifier, Multiplex IHCHALO
Anticoagulants Enhance Molecular and Cellular Immunotherapy of Cancer by Improving Tumor Microcirculation Structure and Function and Redistributing Tumor InfiltratesWei F, Su Y, Quan Y, Li X, Zou Q, Zhang L, Li S, Jiang M, Lin G, Liang P, He J, Xie K2023Clinical Cancer ResearchImmuno-oncologyClassifier, Multiplex IHC, Spatial Analysis, Highplex FLHALO
Apolipoprotein E induces pathogenic senescent-like myeloid cells in prostate cancerBancaro 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 A2023Cancer CellOncologyClassifier, Highplex FLHALO
Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockadePai 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 A2023Cancer CellImmuno-oncologyClassifierHALO
Immune profiling and RNA-seq uncover the cause of partial unexplained recurrent implantation failureFan X, Zhao Q, Li Y, Chen Z, Liao J, Chen H, Meng F, Lu G, Lin G, Gong F2023International ImmunopharmacologyImmunologyClassifier, Multiplex IHCHALO
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
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 ArrowYu S, Diao L, Lian R, Chen C, Huang C, Li X, Li Y, Zeng Y2023Human ReproductionOtherClassifier, Multiplex IHCHALO
Molecular determinants of clinical outcomes of pembrolizumab in recurrent ovarian cancer: Exploratory analysis of KEYNOTE-100Ledermann 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 UA2023Gynecologic OncologyImmuno-oncologyClassifier, Highplex FLHALO
Classification of the tumor immune microenvironment and associations with outcomes in patients with metastatic melanoma treated with immunotherapiesAdegoke 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 J2023Journal for ImmunoTherapy of CancerImmuno-oncologyClassifier, Highplex FLHALO
Empowering Renal Cancer Management with AI and Digital Pathology: Pathology, Diagnostics and PrognosisIvanova E, Fayzullin A, Grinin V, Ermilov D, Arutyunyan A, Timashev P, Shekhter A2023BiomedicinesReviewClassifier, Area Quantification, Object ColocalizationHALO, 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 studyZhou S, Sun D, Mao W, Liu Y, Cen W, Ye L, Liang F, Xu J, Shi H, Ji Y, Wang L, Chang W2023eClinicalMedicineOncologyClassifier, Multiplex IHCHALO
Unaltered hepatic wound healing response in male rats with ancestral liver injuryBeil 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 R2023Nature CommunicationsOtherClassifier, Area QuantificationHALO, HALO AI
Disease pathology signatures in a mouse model of Mucopolysaccharidosis type IIIBPetrova R, Patil AR, Trinh V, McElroy KE, Bhakta M, Tien J, Wilson DS, Warren L, Stratton JR2023Scientific ReportsNeuroscience, MetabolismClassifier, Area Quantification, Object ColocalizationHALO
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 cancerMijit M, Kpenu E, Chowdhury N, Gampala S, Wireman R, Liu S, Babb O, Georgiadis M, Wan J, Fishel M, Kelley M2023Redox BiologyOncologyClassifierHALO
The tumor-derived cytokine Chi3l1 induces neutrophil extracellular traps that promote T cell exclusion in triple-negative breast cancerTaifour 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 WJ2023ImmunityImmuno-oncologyClassifier, Multiplex IHC, Spatial Analysis, Highplex FLHALO
Components of the tumor immune microenvironment based on m-IHC correlate with prognosis and subtype of triple-negative breast cancerLin L, Li H, Wang X, Wang Z, Su G, Zhou J, Sun S, Ma X, Chen Y, You C, Gu Y2023Cancer MedicineImmuno-oncologyClassifier, Spatial Analysis, Highplex FLHALO
CD44 expression in renal tubular epithelial cells in the kidneys of rats with cyclosporine-induced chronic kidney diseaseMatsushita K, Toyoda T, Akane H, Morikawa T, Ogawa K2023Journal of Toxicologic PathologyToxicologyClassifierHALO
Integrated multi-omics profiling to dissect the spatiotemporal evolution of metastatic hepatocellular carcinomaSun 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 J2023Cancer CellOncologyClassifier, Multiplex IHC, Spatial Analysis, Highplex FLHALO
Tumor-associated fibrosis impairs immune surveillance and response to immune checkpoint blockade in non–small cell lung cancerHerzog B, Baer J, Borcherding N, Kingston N, Belle J, Knolhoff B, Hogg G, Ahmad F, Kang L, Petrone J, Lin C, Govindan R, Denardo D2023Science Translational MedicineOncologyClassifier, Multiplex IHCHALO
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 L2023Cancer Prevention ResearchOncologyClassifier, ImmuneHALO
Complex Urban Atmospheres alters Alveolar Stem Cells Niche Properties and drives Lung FibrosisBelgacemi 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 L2023American Journal of Physiology - Lung Cellular and Molecular PhysiologyFibrosisClassifier, Area Quantification, Highplex FLHALO
The tumor microenvironment state associates with response to HPV therapeutic vaccination in patients with respiratory papillomatosisNORBERG 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 C2023Science Translational MedicineOncologyClassifier, Highplex FLHALO, HALO AI
Role of CD44 expressed in renal tubules during maladaptive repair in renal fibrogenesis in an allopurinol-induced rat model of chronic kidney diseaseMatsushita K, Toyoda T, Akane H, Morikawa T, Ogawa K2023Journal of Applied ToxicologyToxicologyClassifierHALO
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 A2023DiabetesGastroenterologyClassifier, Highplex FLHALO
A modified mouse model of Friedreich's ataxia with conditional Fxn allele homozygosity delays onset of cardiomyopathyPerfitt 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 A2023American Journal of Physiology-Heart and Circulatory PhysiologyOtherClassifier, Area QuantificationHALO
Mutant p53 gains oncogenic functions through a chromosomal instability-induced cytosolic DNA responseZhao M, Wang T, Gleber-Netto F O, Chen Z, McGrail D J, Gomez J A, Ju W, Gadhikar M A, Ma W, Shen L, Wang Q, Tang X, Pathak S, Raso M G, Burks J K, Lin S-Y, Wang J, Multani A S, Pickering C R, Chen J, Myers J N, Zhou G2024Nature CommunicationsOncologyClassifier, Multiplex IHCHALO
Early immune remodeling steers clinical response to frontline chemoimmunotherapy in advanced gastric cancerAn M, Mehta A, Min BH, Geo YJ, Wright SJ, Parikh M, Bi L, Lee H, Kim TJ, Lee SY, Moon J, Park RJ, Strickland MR, Park WY, Kang WK, Kim KM, Kim ST, Lempner SJ, Lee J2024Cancer DiscoveryImmuno-oncologyClassifier, Highplex FLHALO
Nanoparticle mediated photodynamic therapy as a method to ablate oral cavity squamous cell carcinoma in preclinical modelsSahovaler A, Valic M, Townson J, Chan H, Zheng M, Tzelnick S, Mondello T, Pener-Tessler A, Eu D, El-Sayes A, Ding L, Chen J, Douglas C, Weersink R, Muhanna N, Zheng G, Irish J2024Cancer ResearchOncologyClassifier, Multiplex IHCHALO
Translational and Therapeutic Evaluation of RAS-GTP Inhibition by RMC-6236 in RAS-Driven CancersJiang J, Jiang L, Maldonato B J, Wang Y, Holderfield M, Aronchik I, Winters I P, Salman Z, Blaj C, Menard M, Brodbeck J, Chen Z, Wei X, Rosen M J, Gindin Y, Lee B J, Evans J W, Chang S, Wang Z, Seamon K J, Parsons D, Cregg J, Marquez A, Tomlinson A C A, Yano J K, Knox J E, Quintana E, Aguirre A J, Arbour K C, Reed A, Gustafson W C, Gill A L, Koltun E S, Wildes D, Smith J A M, Wang Z, Singh M2024Cancer DiscoveryOncologyClassifier, Area Quantification, CytonuclearHALO
Tertiary lymphoid structures and B cells determine clinically relevant T cell phenotypes in ovarian cancerKasikova L, Rakova J, Hensler M, Lanickova T, Tomankova J, Pasulka J, Drozenova J, Mojzisova K, Fialova A, Vosahlikova S, Laco J, Ryska A, Dundr P, Kocian R, Brtnicky T, Skapa P, Capkova L, Kovar M, Prochazka J, Praznovec I, Koblizek V, Taskova A, Tanaka H, Lischke R, Mendez F C, Jr J V, Heinzelmann-Schwarz V, Jacob F, McNeish I A, Halaska M J, Rob L, Cibula D, Orsulic S, Galluzzi L, Spisek R, Fucikova J2024Nature CommunicationsOncologyClassifier, Highplex FL, RegistrationHALO

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