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HALO® Module

Spatial Analysis

Particularly useful to those involved in the immune-oncology field, the Spatial Analysis module offers a suite of subsequent analysis tools which can be used to identify proximity and relative spatial distribution of objects, cells, and/or features across single tissues or serial sections. This module is embedded within the HALO platform and can be used in conjunction with any of our cell-based analysis modules for brightfield or fluorescence.

Nearest Neighbor

Determine the average distance and number of unique neighbors between any two cell or object populations.  The example below depicts pan cytokeratin positive cells (blue) and CD4 positive cells (red). Grey lines connect each CD4 positive cell to the nearest pan cytokeratin positive cell.

Proximity Analysis

Calculate the number of objects or cells within a certain distance of another object or cell.  In the example below, the distance is set to 30 microns. CD8 positive cells within 30 microns of a pan cytokeratin positive cell (blue) are labeled green and CD8 positive cells greater than 30 microns from pan cytokeratin positive cell are labeled purple. A corresponding proximity histogram is automatically generated.

Infiltration Analysis

Determine the number of objects or cells within a set range of an annotated region of interest.  Depicted below is a whole slide image stained with CD8. The tumor boundary has been defined/annotated in green.  The infiltration analysis tool defines the invasive margin inside of tumor (yellow and red) and the invasive margin outside of the tumor (blue and purple) automatically. In this example, the distance is set to 500 microns around the annotated tumor boundary.  CD8 positive cells are quantified within the margin. A histogram is automatically generated to reflect CD8+ cell density inside the tumor boundary (-1 to -500), at the tumor boundary (0), and outside the tumor boundary (+1 to +500) as shown in the image below.

Density Heatmaps

The density heatmap spatial analysis algorithm measures the density of a selected cell population from your object data within a certain radius. The scaling and colors of the markup are customizable. Reported in the summary data, the entire tissue area is analyzed and all cells of the desired population are counted. The average cell population and the average cell population density is calculated within the user-defined radius, as well as the minimum and maximum densities.

The tissue below is stained with an immune cell marker (red stain) and a tumor marker (DAB stain).  The image was analyzed with the Multiplex IHC module to detect positivity and produce object data. The density heatmap analysis was used with a radius of 25 microns, measuring the density of immune cell positivity across the whole slide. The markup image, with adjustable transparency, depicts areas of higher density in red and orange, moderate density in yellow, and areas of lower density in green and blue.

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

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.

Characterizing the Cellular Architecture of the Tumor Microenvironment Using Imaging Mass Cytometry and Digital Image Analysis with the HALO® and HALO AI Platform

In this application note, we describe how HALO Highplex FL module, HALO AI and spatial analysis can be used in a convenient workflow for analysis of the TME and highly multiplexed IMC images.

Publication Spotlight

The table below includes publications that cite the Spatial Analysis module. 

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

TitleAuthorsYearJournalApplicationHALO ModulesProduct
Progranulin mediates immune evasion of pancreatic ductal adenocarcinoma through regulation of MHCI expressionCheung P, Yang J, Fang R, Borgers A, Krengel K, Stoffel A, Althoff K, Yip C, Siu E, Ng L, Lang K, Cham L, Engel D, Soun C, Cima I, Scheffler B, Striefler J, Sinn M, Bahra M, Pelzer U, Oettle H, Markus P, Smeets E, Aarntzen E, Savvatakis K, Liffers S, Lueong S, Neander C, Bazarna A, Zhang X, Paschen A, Crawford H, Chan A, Cheung S, Siveke J2022Nature CommunicationsOncologyCytonuclear, Spatial Analysis, Highplex FLHALO
Tumor cell-derived exosomes deliver TIE2 protein to macrophages to promote angiogenesis in cervical cancerDu S, Qian J, Tan S, Li W, Liu P, Zhao J, Zeng Y, Xu L, Wang Z, Cai J2022Cancer LettersOncologyArea Quantification, Cytonuclear, Spatial Analysis, Highplex FLHALO
Intratumoural spatial distribution of S100B?+?folliculostellate cells is associated with proliferation and expression of FSH and ER? in gonadotroph tumoursIlie M, Vasiljevic A, Chanal M, Gadot N, Chinezu L, Jouanneau E, Hennino A, Raverot G, Bertolino P2022Acta Neuropathologica CommunicationsOncologyCytonuclear, Spatial AnalysisHALO
Interspatial Distribution of Tumor and Immune Cells in Correlation with PD-L1 in Molecular Subtypes of Gastric CancersDislich B, Mertz K, Gloor B, Langer R2022CancersImmuno-oncologyMultiplex IHC, Spatial Analysis, Figure MakerHALO
Peritumoral TIGIT+CD20+†B cell infiltration indicates poor prognosis but favorable adjuvant chemotherapeutic response in gastric cancerLiu H, Wu J, Xu X, Wang H, Zhang C, Yin S, He Y2022International ImmunopharmacologyOncologyCytonuclear, Spatial Analysis, Highplex FLHALO
SPOP promotes cervical cancer progress by inducing PD-1 move away from PD-L1 in spatial localizationWu J, Wu Y, Guo Q, Chen S, Wang S, Zhu J, Wu X, Ju X2022Research SquareOncologyCytonuclear, Spatial Analysis, Highplex FL, TMAHALO
Higher proportions of CD39+ tumorresident cytotoxic T cells predict recurrence-free survival in patients with stage III melanoma treated with adjuvant immunotherapyAttrill G, Owen C, Ahmed T, Vergara I, Colebatch A, Conway J, Nahar K, Thompson J, da Silva I, Carlino M, Menzies A, Lo S, Palendira U, Scolyer R, Long G, Wilmott J2022Journal of Immuno Therapy of CancerImmuno-oncologyCytonuclear, Spatial Analysis, Highplex FLHALO
gp96 Expression in Gliomas and Its Association with Tumor Malignancy and T Cell Infiltrating LevelLi C, Wang Y, Long L, Zhang P, Zhang Y, Ji N2022Hindawi Journal of OncologyImmuno-oncologySpatial Analysis, Highplex FL, Figure MakerHALO
Spartalizumab or placebo in combination with dabrafenib and trametinib in patients with†BRAF†V600-mutant melanoma: exploratory biomarker analyses from a randomized phase 3 trial (COMBI-i)Tawbi H, Robert C, Brase J, Gusenleitner D, Gasal E, Garrett J, Savchenko A, Gorgun G, Flaherty K, Ribas A, Dummer R, Schadendorf D, Long G, Nathan P, Ascierto P2022Journal for ImmunoTherapy of CancerOncologyMultiplex IHC, Spatial AnalysisHALO
Endothelial cell death after ionizing radiation does not impair vascular structure in mouse tumor modelsKaeppler J, Chen J, Buono M, Vermeer J, Kannan P, Cheng W, Voukantsis D, Thompson J, Hill M, Allen D, Gomes A, Kersemans V, Kinchesh P, Smart S, Buffa F, Nerlov C, Muschel R, Markelc B2022EMBO ReportsOncologySpatial Analysis, Highplex FLHALO
Approaches to spatially resolving the tumour immune microenvironment of hepatocellular carcinomaMarsh-Wakefield F, Ferguson A, Liu K, Santhakumar C, McCaughan G, Palendira U2022Therapeutic Advances in Medical OncologyReviewMultiplex IHC, Spatial Analysis, Highplex FLHALO
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
Tau Pathology in Chronic Traumatic Encephalopathy is Primarily NeuronalButler M, Dixon E, Stein T, Alvarez V, Huber B, Buckland M, McKee A, Cherry J2022Journal of Neuropathology & Experimental NeurologyNeuroscienceMultiplex IHC, Spatial Analysis, Highplex FLHALO, HALO AI
Chemoradiation-induced alteration of programmed death-ligand 1, CD8+ tumor-infiltrating lymphocytes and mucin expression in rectal cancerBaretti M, Zhu Q, Fu W, Meyer J, Wang H, Anders R, Azad N2022OncotargetOncologyMultiplex IHC, Spatial AnalysisHALO
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
Haploinsufficiency of the lysosomal sialidase†NEU1†results in a model of pleomorphic rhabdomyosarcoma in miceMachado E, van de Vlekkert D, Sheppard H, Perry S, Downing S, Laxton J, Ashmun R, Finkelstein D, Neale G, Hu H, Harwood F, Koo S, Grosveld G, d'Azzo A2022Communications BiologyOncologyMembrane, Spatial AnalysisHALO
Fibrocytes boost tumor-supportive phenotypic switches in the lung cancer niche via the endothelin systemWeigert A, Zheng X, Nenzel A, Turkowski K, Gunther S, Strack E, Sirait-Fischer E, Elwakeel E, Kur I, Nikam V, Valasarajan C, Winter H, Wissgott A, Voswinkel R, Grimminger F, Brune B, Seeger W, Pullamsetti S, Savai R2022Nature CommunicationsOncologySpatial Analysis, Highplex FLHALO
Use of High-Plex Data Reveals Novel Insights into the Tumour Microenvironment of Clear Cell Renal Cell CarcinomaDe Filippis R, Wolflein G, Um I, Caie P, Warren S, White A, Suen E, To E, Arandjelovic O, Harrison D2022CancersOncologySpatial AnalysisHALO, HALO AI
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
Annexin A2/TLR2/MYD88 pathway induces arginase 1 expression in tumor-associated neutrophilsZhang H, Zhu X, Friesen T, Kwak J, Pisarenko T, Mekvanich S, Velasco M, Randolph T, Kargl J, Houghton A2022Journal of Clinical InvestigationImmuno-oncologySpatial Analysis, ISH-IHC/FISH-IFHALO
Impact of HPV status on immune responses in head and neck squamous cell carcinomaQureshi H, Zhu X, Yang G, Steadele M, Pierce R, Futran N, Lee S, Mendez E, Houghton A2022Oral OncologyOncologyMultiplex IHC, Spatial Analysis, Highplex FLHALO
Developing a Nomogram for Preoperative Prediction of Cervical Cancer Lymph Node Metastasis by Multiplex ImmunofluorescenceWu J, Guo Q, Zhu J, Wu Y, Liang S Chen S, Wang S, Ju X, Wu X2022AuthoreaOncologySpatial Analysis, Highplex FL, TMAHALO
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
Neoantigen-specific CD4+ T cells in human melanoma have diverse differentiation states and correlate with CD8+ T cell, macrophage, and B cell functionVeatch J, Lee S, Shasha C, Singhi N, Szeto J, Moshiri A, Kim T, Smythe K, Kong P, Fitzgibbon M, Jesernig B, Bhatia S, Tykodi S, Hall E, Byrd D, Thompson J, Pillarisetty V, Duhen T, Houghton A, Newell E, Gottardo R, Riddell S2022Cancer CellImmuno-oncologySpatial Analysis, Highplex FLHALO
Escherichia coli-specific CXCL13-producing TFH are associated with clinical efficacy of neoadjuvant PD-1 blockade against muscle-invasive bladder cancerGoubet A, Lordello L, Silva C, Peguillet I, Gazzano M, Mbogning-Fonkou M, Thelemaque C, Lebacle C, Thibault C, Audenet F, Pignot G, Gravis G, Helissey C, Campbedel L, Roupret M, Xylinas E, Ouzaid I, Dubuisson A, Mazzenga M, Flament C, Ly P, Marty V, Signolle N, Sauvat A, Sbarrato T, Filahi M, Davin C, Haddad G, Khalil J, Bleriot C, Danlos F, Dunsmore G, Mulder K, Silvin A, Raoult T, Archambaud B, Belhechmi S, Boneca I, Cayet N, Moya-Nilges M, Mallet A, Daillere R, Rouleau E, Radulescu C, Allory Y, Fieschi J, Rouanne M, Ginhoux F, Le Teuff G, Derosa L, Marabelle A, Van Dorp J, Van Dijk N, van der Heijden M, Besse B, Andre F, Merad M, Kroemer G, Scoazec J, Zitvogel L, Loriot Y2022Cancer DiscoveryOncologyMultiplex IHC, Spatial AnalysisHALO
Upfront FOLFOXIRI plus bevacizumab with or without atezolizumab in the treatment of patients with metastatic colorectal cancer (AtezoTRIBE): a multicentre, open-label, randomised, controlled, phase 2 trialAntoniotti C, Rossini D, Pietrantonio F, Catteau A, Salvatore L, Lonardi S, Boquet I, Tamberi S, Marmorino F, Moretto R, Ambrosini M, Tamburini E, Tortora G, Passardi A, Bergamo F, Kassambara A, Sbarrato T, Morano F, Ritorto G, Borelli B, Boccaccino A, Conca V, Giordano M, Ugolini C, Fieschi J, Papadopulos A, Massoue C, Aprile G, Antonyzzo L, Gelsomino F, Martinelli E, Pella N, Masi G, Fontanini G, Boni L, Galon J, Cremolini C2022The Lancet OncologyOncologyMultiplex IHC, Spatial AnalysisHALO
Plasma CD27, a surrogate of the intratumoral CD27-CD70 interaction, correlates with immunotherapy resistance in renal cell carcinomaBenhamouda N, Sam I, Epaillard N, Gey A, Phan L, Pham H, Gruel N, Saldmann A, Pineau J, Hasan M, Quiniou V, Nevoret C, Verkarre V, Libri V, Mella S, Granier C, Broudin C, Ravel P, De Guillebon E, Mauge L, Helley D, Jabla B, Chaput N, Albiges L, Katsahian S, Adam J, Mejean A, Adotevi O, Vano Y, Oudard S, Tartour E2022Clinical Cancer ResearchOncologySpatial Analysis, Highplex FLHALO
High endothelial venules associated with better prognosis in esophageal squamous cell carcinomaLi H, Tang L, Han X, Zhong L, Gao W, Chen Y, Huang J, Wen Z2022Annals of Diagnostic PathologyOncologyObject Colocalization, Spatial Analysis, Highplex FLHALO
Defactinib, pembrolizumab, and gemcitabine in patients with advanced treatment refractory pancreatic cancer: A phase I, dose escalation, and expansion studyWang-Gillam A, Lim K, McWilliams R, Suresh R, Lockhart A, Brown A, Breden M, Belle J, Herndon J, Bogner S, Pedersen K, Tan B, Boice N, Acharya A, Abdiannia M, Gao F, Yoon H, Zhu M, Trikalinos N, Ratner L, Aranha O, Hawkins W, Herzog B, DeNardo D2022Clinical Cancer ResearchImmuno-oncologyMultiplex IHC, Spatial AnalysisHALO
Th1-involved immune infiltrates improve neoadjuvant chemoradiotherapy response of esophageal squamous cell carcinomaYuan J, Weng Z, Tan Z, Luo K, Zhong J, Xie X, Qu C, Lin X, Yang H, Wen J, Fu J2022Cancer LettersImmuno-oncologyMultiplex IHC, Spatial AnalysisHALO
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
Autologous T cell therapy for MAGE-A4+ solid cancers in HLA-A*02+ patients: a phase 1 trialHong D, Van Tine B, Biswas S, McAlpine C, Johnson M, Olszanski A, Clarke J, Araujo D, Blumenschein G, Kebriaei P, Lin Q, Tipping A, Sanderson J, Wang R, Trivedi T, Annareddy T, Bai J, Rafail S, Sun A, Fernandes L, Navenot J-M, Bushman F, Everett J, Karadeniz D, Broad R, Isabelle M, Naidoo R, Bath N, Betts G, Wolchinsky Z, Batrakou D, Van Winkle E, Elefant E, Ghobadi A, Cashen A, Grand'Maison A, McCarthy P, Fracasso P, Norry E, Williams D, Druta M, Liebner D, Odunsi K, Butler M2023Nature MedicineImmuno-oncologyISH/FISH, Spatial Analysis, Highplex FLHALO
CD8+ Cell Density Gradient across the Tumor Epithelium–Stromal Interface of Non-Muscle Invasive Papillary Urothelial Carcinoma Predicts Recurrence-Free Survival after BCG ImmunotherapyDrachneris J, Rasmusson A, Morkunas M, Fabijonavicius M, Cekauskas A, Jankevicius F, Laurinavicius A2023CancersImmuno-oncologyMultiplex IHC, Spatial Analysis, HALO AIHALO
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
Co-enrichment of CD8-positive T cells and macrophages is associated with clinical benefit of tislelizumab in solid tumorsYe D, Desai J, Shi J, Liu S, Shen W, Liu T, Shi Y, Wang D, Liang L, Yang S, Ma X, Jin W, Zhang P, Huang R, Shen Z, Zhang Y, Wu Y2023Biomarker ResearchImmuno-oncologySpatial Analysis, Highplex FLHALO
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
The localization of molecularly distinct microglia populations to Alzheimer's disease pathologies using QUIVERShahidehpour R, Nelson A, Sanders L, Embry C, Nelson P, Bachstetter A2023Acta Neuropathologica CommunicationsNeuroscienceArea Quantification, Object Colocalization, Spatial Analysis, Registration
Development of a deep pathomics score for predicting hepatocellular carcinoma recurrence after liver transplantationQu W, Tian M, Lu G, Zhou Y, Liu W, Tang Z, Yao Z, Huang R, Zhu G, Jiang X, Tao C, Fang Y, Gao J, Wu X, Chen J, Zhao Q, Yang R, Chu T, Zhou J, Fan J, Yu J, Shi Y2023Hepatology InternationalOncologySpatial Analysis, Highplex FLHALO
An Immune-Related Gene Expression Signature Predicts Benefit from Adding Atezolizumab to FOLFOXIRI plus Bevacizumab in Metastatic Colorectal CancerAntoniotti C, Boccaccino A, Seitz R, Giordano M, Catteau A, Rossini D, Pietrantonio F, Salvatore L, McGregor K, Bergamo F, Conca V, Leonetti S, Morano F, Papiani G, Tamburini E, Bensi M, Murgioni S, Ross D, Passardi A, Boquet I, Nielsen T, Galon J, Varga M, Schweitzer B, and Cremolini C2023Clinical Cancer ResearchImmuno-oncologyMultiplex IHC, Spatial AnalysisHALO
Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancerWang F, Long J, Li L, Wu Z, Da T, Wang X, Huang C, Jiang Y, Yao X, Ma H, Lian Z, Zhao Z, Cao J2023Science AdvancesOncologyMultiplex IHC, Spatial Analysis, Highplex FLHALO
Dissecting tumor lymphocyte infiltration to predict benefit from immune-checkpoint inhibitors in metastatic colorectal cancer: lessons from the AtezoTRIBE studyMoretto R, Rossini D, Catteau A, Antoniotti C, Giordano M, Boccaccino A, Ugolini C, Proietti A, Conca V, Kassambara A, Pietrantonio F, Salvatore L, Lonardi S, Tamberi S, Tamburini E, Poma A, Fieschi J, Fontanini G, Masi G, Galon J, Cremolini C2023Journal for ImmunoTherapy of CancerImmuno-oncologyMultiplex IHC, Spatial AnalysisHALO
High tumor mutational burden predicts favorable response to anti-PD-(L)1 therapy in patients with solid tumor: a real-world pan-tumor analysisJung J, Heo Y, Park S2023Journal for ImmunoTherapy of CancerImmuno-oncologySpatial Analysis, Highplex FLHALO
Immunoscore immune checkpoint using spatial quantitative analysis of CD8 and PD-L1 markers is predictive of the efficacy of anti- PD1/PD-L1 immunotherapy in non-small cell lung cancerGhiringhelli F, Bibeau F, Greillier L, Fumet J, Ilie A, Monville F, Laugé C, Catteau A, Boquet I, Majdi A, Morgand E, Oulkhouir Y, Brandone N, Adam J, Sbarrato T, Kassambara A, Fieschi J, Garcia S, Lepage A, Tomasini P, Galon J2023EBioMedicineImmuno-oncologyMultiplex IHC, Spatial AnalysisHALO
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
The Hippo-YAP signaling pathway drives CD24- mediated immune evasion in esophageal squamous cell carcinoma via macrophage phagocytosisYan Z, Hou J, Zhang L, Chen Z, Gao C, Ahmad N, Guo M, Wang W, Han T, Chang T, Kang X, Wang L, Liang Y, Li X, Zhou X2023Research SquareImmuno-oncologySpatial AnalysisHALO
Stem cell-like T cell depletion in the recurrent head and neck cancer immune microenvironmentChen L, Lee N, Sarkar R, Katabi N, Li Y, Morris L, Wong R, Sherman E, Reis-Filho J, Hollmann T, Riaz N2023OncoImmunologyImmuno-oncologySpatial Analysis, Highplex FLHALO
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
Multiplex Immunohistochemistry and Immunofluorescence: A Practical Update for PathologistsHarms P, Frankel T, Moutafi M, Rao A, Rimm D, Taube J, Thomas D, Chang M, Pantanowitz L2023Modern PathologyReviewSpatial Analysis, Highplex FLHALO
Neighboring macrophage-induced alteration in the phenotype of colorectal cancer cells in the tumor budding areaKawamura I, Ohe R, Suzuki K, Kabasawa T, Kitoaka T, Takahara D, Kono M, Uchiyama N, Musha H, Futakuchi M, Motoi F2023Research SquareImmuno-oncologyMultiplex IHC, Spatial AnalysisHALO
Single-cell RNA-sequencing reveals heterogeneity and intercellular crosstalk in human tuberculosis lungWang, H, Wen, Z, Niu, L, Chen, X, Liu, H, Zhang, S, Xu, J, Zhu, Y, Li, H, Chen, H, Shi, L, Wan, L, Li, L, Li, M, Wong, K, Song, Y2023Journal of InfectionImmunology, Infectious DiseaseSpatial Analysis, Highplex FLHALO
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
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
Spatial mapping reveals granuloma diversity and histopathological superstructure in human tuberculosisSawyer A, Patrick E, Edwards J, Wilmott J, Fielder T, Yang Q, Barber D, Ernst J, Britton W, Palendira U, Chen X, Feng C2023Journal of Experimental MedicineImmunologyMultiplex IHC, Spatial Analysis, Highplex FLHALO
Spatial Proximity and Relative Distribution of Tumor-Infiltrating Lymphocytes and Macrophages Predict Survival in MelanomaDe Logu F, Ugolini F, Iannone L F, Simi S, Maio V, de Giorgi V, di Giacomo A M, Miracco C, Cossu A, Palmieri G, Mandalà M, Massi D2023Laboratory InvestigationOncologyMultiplex IHC, Spatial AnalysisHALO, HALO Link

Related HALO Modules

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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Object Colocalization

Count one or two objects and measure the object area, diameter, stain intensity, and colocalization (where applicable). Microvessel and amyloid plaque quantification are most common applications.

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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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