Before Markup

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)
  • KFBIO (KFB, KFBF)
  • 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.

Characterizing the TME using IMC and HALO® Image Analysis

See in this app note how automated analysis of highly multiplexed IMC images using HALO and HALO AI yields rich cellular and spatial data from a streamlined workflow.

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

HiPlex RNAscope™ Application Note

Using our FISH module we demonstrate how to perform 12-plex RNAscope image analysis using ACD’s HiPlexv2 assay.

RNAscope™ Image Analysis Using HALO and HALO AI

Using our ISH module for brightfield and our FISH module for fluorescence, we demonstrate how to quantify ISH signal from RNAscope™ assays based on ACD Bio’s recommended scoring guidelines.

Depicting TME Cellular Architecture Using Hyperplex IF and Automated Image Analysis

Download our eBook in collaboration with Lunaphore to learn more about how Pharma Services depicted TME cellular architecture using hyperplex IF and automated image analysis.

Lunaphore COMET Hyperplex IF and HALO® Image Analysis of the TME

Download our collaborative poster with Lunaphore to see how HALO and HALO AI, alongside the Lunaphore COMET instrument, enable a high throughput workflow for phenotypic and spatial analysis of cells in the tumor microenvironment.

Characterizing the TME using IMC and HALO® Image Analysis

See in this app note how automated analysis of highly multiplexed IMC images using HALO and HALO AI yields rich cellular and spatial data from a streamlined workflow.

Automated Tumor Budding Quantification in Colorectal Carcinoma H&E Images

Learn about quantification of tumor budding in colorectal carcinoma using HALO and HALO AI.

Quantitative Image Analysis of a Combined FISH-IF Assay

Learn how to detect protein and RNA in a single assay using ACD’s Co-Detection workflow and HALO image analysis.

Spatial Characterization of the TME with Cell DIVE Multiplexed Imaging and HALO Image Analysis

Check out our collaborative poster with Cell Signaling Technology and Leica Microsystems to learn about a combined workflow for spatial analysis of the TME.

Spatial Multiplex Profiling of Immune Markers with the RNAscope Hiplex v2 Assay

Download this poster to learn about combining ACD’s HiPlex v2 in situ hybridization assay with HALO image analysis.

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 Spatial Analysis module. 

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

Title Authors Year Journal Application HALO Modules Product
Progranulin mediates immune evasion of pancreatic ductal adenocarcinoma through regulation of MHCI expression Cheung 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 J 2022 Nature Communications Oncology Cytonuclear, Spatial Analysis, Highplex FL HALO
Tumor cell-derived exosomes deliver TIE2 protein to macrophages to promote angiogenesis in cervical cancer Du S, Qian J, Tan S, Li W, Liu P, Zhao J, Zeng Y, Xu L, Wang Z, Cai J 2022 Cancer Letters Oncology Area Quantification, Cytonuclear, Spatial Analysis, Highplex FL HALO
Intratumoural spatial distribution of S100B?+?folliculostellate cells is associated with proliferation and expression of FSH and ER? in gonadotroph tumours Ilie M, Vasiljevic A, Chanal M, Gadot N, Chinezu L, Jouanneau E, Hennino A, Raverot G, Bertolino P 2022 Acta Neuropathologica Communications Oncology Cytonuclear, Spatial Analysis HALO
Interspatial Distribution of Tumor and Immune Cells in Correlation with PD-L1 in Molecular Subtypes of Gastric Cancers Dislich B, Mertz K, Gloor B, Langer R 2022 Cancers Immuno-oncology Multiplex IHC, Spatial Analysis, Figure Maker HALO
Peritumoral TIGIT+CD20+†B cell infiltration indicates poor prognosis but favorable adjuvant chemotherapeutic response in gastric cancer Liu H, Wu J, Xu X, Wang H, Zhang C, Yin S, He Y 2022 International Immunopharmacology Oncology Cytonuclear, Spatial Analysis, Highplex FL HALO
SPOP promotes cervical cancer progress by inducing PD-1 move away from PD-L1 in spatial localization Wu J, Wu Y, Guo Q, Chen S, Wang S, Zhu J, Wu X, Ju X 2022 Research Square Oncology Cytonuclear, Spatial Analysis, Highplex FL, TMA HALO
Higher proportions of CD39+ tumorresident cytotoxic T cells predict recurrence-free survival in patients with stage III melanoma treated with adjuvant immunotherapy Attrill 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 J 2022 Journal of Immuno Therapy of Cancer Immuno-oncology Cytonuclear, Spatial Analysis, Highplex FL HALO
gp96 Expression in Gliomas and Its Association with Tumor Malignancy and T Cell Infiltrating Level Li C, Wang Y, Long L, Zhang P, Zhang Y, Ji N 2022 Hindawi Journal of Oncology Immuno-oncology Spatial Analysis, Highplex FL, Figure Maker HALO
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 P 2022 Journal for ImmunoTherapy of Cancer Oncology Multiplex IHC, Spatial Analysis HALO
Endothelial cell death after ionizing radiation does not impair vascular structure in mouse tumor models Kaeppler 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 B 2022 EMBO Reports Oncology Spatial Analysis, Highplex FL HALO
Approaches to spatially resolving the tumour immune microenvironment of hepatocellular carcinoma Marsh-Wakefield F, Ferguson A, Liu K, Santhakumar C, McCaughan G, Palendira U 2022 Therapeutic Advances in Medical Oncology Review Multiplex IHC, Spatial Analysis, Highplex FL 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
Tau Pathology in Chronic Traumatic Encephalopathy is Primarily Neuronal Butler M, Dixon E, Stein T, Alvarez V, Huber B, Buckland M, McKee A, Cherry J 2022 Journal of Neuropathology & Experimental Neurology Neuroscience Multiplex IHC, Spatial Analysis, Highplex FL HALO, HALO AI
Chemoradiation-induced alteration of programmed death-ligand 1, CD8+ tumor-infiltrating lymphocytes and mucin expression in rectal cancer Baretti M, Zhu Q, Fu W, Meyer J, Wang H, Anders R, Azad N 2022 Oncotarget Oncology Multiplex IHC, Spatial Analysis 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
Haploinsufficiency of the lysosomal sialidase†NEU1†results in a model of pleomorphic rhabdomyosarcoma in mice Machado 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 A 2022 Communications Biology Oncology Membrane, Spatial Analysis HALO
Fibrocytes boost tumor-supportive phenotypic switches in the lung cancer niche via the endothelin system Weigert 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 R 2022 Nature Communications Oncology Spatial Analysis, Highplex FL HALO
Use of High-Plex Data Reveals Novel Insights into the Tumour Microenvironment of Clear Cell Renal Cell Carcinoma De Filippis R, Wolflein G, Um I, Caie P, Warren S, White A, Suen E, To E, Arandjelovic O, Harrison D 2022 Cancers Oncology Spatial Analysis HALO, HALO AI
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
Annexin A2/TLR2/MYD88 pathway induces arginase 1 expression in tumor-associated neutrophils Zhang H, Zhu X, Friesen T, Kwak J, Pisarenko T, Mekvanich S, Velasco M, Randolph T, Kargl J, Houghton A 2022 Journal of Clinical Investigation Immuno-oncology Spatial Analysis, ISH-IHC/FISH-IF HALO
Impact of HPV status on immune responses in head and neck squamous cell carcinoma Qureshi H, Zhu X, Yang G, Steadele M, Pierce R, Futran N, Lee S, Mendez E, Houghton A 2022 Oral Oncology Oncology Multiplex IHC, Spatial Analysis, Highplex FL HALO
Developing a Nomogram for Preoperative Prediction of Cervical Cancer Lymph Node Metastasis by Multiplex Immunofluorescence Wu J, Guo Q, Zhu J, Wu Y, Liang S Chen S, Wang S, Ju X, Wu X 2022 Authorea Oncology Spatial Analysis, Highplex FL, TMA HALO
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
Neoantigen-specific CD4+ T cells in human melanoma have diverse differentiation states and correlate with CD8+ T cell, macrophage, and B cell function Veatch 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 S 2022 Cancer Cell Immuno-oncology Spatial Analysis, Highplex FL HALO
Escherichia coli-specific CXCL13-producing TFH are associated with clinical efficacy of neoadjuvant PD-1 blockade against muscle-invasive bladder cancer Goubet 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 Y 2022 Cancer Discovery Oncology Multiplex IHC, Spatial Analysis HALO
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 trial Antoniotti 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 C 2022 The Lancet Oncology Oncology Multiplex IHC, Spatial Analysis HALO
Plasma CD27, a surrogate of the intratumoral CD27-CD70 interaction, correlates with immunotherapy resistance in renal cell carcinoma Benhamouda 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 E 2022 Clinical Cancer Research Oncology Spatial Analysis, Highplex FL HALO
High endothelial venules associated with better prognosis in esophageal squamous cell carcinoma Li H, Tang L, Han X, Zhong L, Gao W, Chen Y, Huang J, Wen Z 2022 Annals of Diagnostic Pathology Oncology Object Colocalization, Spatial Analysis, Highplex FL HALO
Defactinib, pembrolizumab, and gemcitabine in patients with advanced treatment refractory pancreatic cancer: A phase I, dose escalation, and expansion study Wang-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 D 2022 Clinical Cancer Research Immuno-oncology Multiplex IHC, Spatial Analysis HALO
Th1-involved immune infiltrates improve neoadjuvant chemoradiotherapy response of esophageal squamous cell carcinoma Yuan J, Weng Z, Tan Z, Luo K, Zhong J, Xie X, Qu C, Lin X, Yang H, Wen J, Fu J 2022 Cancer Letters Immuno-oncology Multiplex IHC, Spatial Analysis HALO
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
Autologous T cell therapy for MAGE-A4+ solid cancers in HLA-A*02+ patients: a phase 1 trial Hong 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 M 2023 Nature Medicine Immuno-oncology ISH/FISH, Spatial Analysis, Highplex FL HALO
CD8+ Cell Density Gradient across the Tumor Epithelium–Stromal Interface of Non-Muscle Invasive Papillary Urothelial Carcinoma Predicts Recurrence-Free Survival after BCG Immunotherapy Drachneris J, Rasmusson A, Morkunas M, Fabijonavicius M, Cekauskas A, Jankevicius F, Laurinavicius A 2023 Cancers Immuno-oncology Multiplex IHC, Spatial Analysis, HALO AI 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
Co-enrichment of CD8-positive T cells and macrophages is associated with clinical benefit of tislelizumab in solid tumors Ye 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 Y 2023 Biomarker Research Immuno-oncology Spatial Analysis, Highplex FL 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
The localization of molecularly distinct microglia populations to Alzheimer's disease pathologies using QUIVER Shahidehpour R, Nelson A, Sanders L, Embry C, Nelson P, Bachstetter A 2023 Acta Neuropathologica Communications Neuroscience Area Quantification, Object Colocalization, Spatial Analysis, Registration
Development of a deep pathomics score for predicting hepatocellular carcinoma recurrence after liver transplantation Qu 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 Y 2023 Hepatology International Oncology Spatial Analysis, Highplex FL HALO
An Immune-Related Gene Expression Signature Predicts Benefit from Adding Atezolizumab to FOLFOXIRI plus Bevacizumab in Metastatic Colorectal Cancer Antoniotti 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 C 2023 Clinical Cancer Research Immuno-oncology Multiplex IHC, Spatial Analysis HALO
Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer Wang F, Long J, Li L, Wu Z, Da T, Wang X, Huang C, Jiang Y, Yao X, Ma H, Lian Z, Zhao Z, Cao J 2023 Science Advances Oncology Multiplex IHC, Spatial Analysis, Highplex FL HALO
Dissecting tumor lymphocyte infiltration to predict benefit from immune-checkpoint inhibitors in metastatic colorectal cancer: lessons from the AtezoTRIBE study Moretto 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 C 2023 Journal for ImmunoTherapy of Cancer Immuno-oncology Multiplex IHC, Spatial Analysis HALO
High tumor mutational burden predicts favorable response to anti-PD-(L)1 therapy in patients with solid tumor: a real-world pan-tumor analysis Jung J, Heo Y, Park S 2023 Journal for ImmunoTherapy of Cancer Immuno-oncology Spatial Analysis, Highplex FL HALO
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 cancer Ghiringhelli 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 J 2023 EBioMedicine Immuno-oncology Multiplex IHC, Spatial Analysis 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
The Hippo-YAP signaling pathway drives CD24- mediated immune evasion in esophageal squamous cell carcinoma via macrophage phagocytosis Yan 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 X 2023 Research Square Immuno-oncology Spatial Analysis HALO
Stem cell-like T cell depletion in the recurrent head and neck cancer immune microenvironment Chen L, Lee N, Sarkar R, Katabi N, Li Y, Morris L, Wong R, Sherman E, Reis-Filho J, Hollmann T, Riaz N 2023 OncoImmunology Immuno-oncology Spatial Analysis, Highplex FL HALO
Differential expression of CD8 defines phenotypically distinct cytotoxic T cells in cancer and multiple sclerosis Burkard T, Herrero San Juan M, Dreis C, Kiprina A, Namgaladze D, Siebenbrodt K, Luger S, Foerch C, Pfeilschifter J, Weigert A, Radeke H 2023 Clinical and Translational Medicine Oncology, immunology Classifier, Spatial Analysis, Highplex FL, TMA HALO
Multiplex Immunohistochemistry and Immunofluorescence: A Practical Update for Pathologists Harms P, Frankel T, Moutafi M, Rao A, Rimm D, Taube J, Thomas D, Chang M, Pantanowitz L 2023 Modern Pathology Review Spatial Analysis, Highplex FL HALO
Neighboring macrophage-induced alteration in the phenotype of colorectal cancer cells in the tumor budding area Kawamura I, Ohe R, Suzuki K, Kabasawa T, Kitoaka T, Takahara D, Kono M, Uchiyama N, Musha H, Futakuchi M, Motoi F 2023 Research Square Immuno-oncology Multiplex IHC, Spatial Analysis HALO
Single-cell RNA-sequencing reveals heterogeneity and intercellular crosstalk in human tuberculosis lung Wang, 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, Y 2023 Journal of Infection Immunology, Infectious Disease Spatial Analysis, Highplex FL 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
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
Spatial mapping reveals granuloma diversity and histopathological superstructure in human tuberculosis Sawyer A, Patrick E, Edwards J, Wilmott J, Fielder T, Yang Q, Barber D, Ernst J, Britton W, Palendira U, Chen X, Feng C 2023 Journal of Experimental Medicine Immunology Multiplex IHC, Spatial Analysis, Highplex FL HALO
Spatial Proximity and Relative Distribution of Tumor-Infiltrating Lymphocytes and Macrophages Predict Survival in Melanoma De 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 D 2023 Laboratory Investigation Oncology Multiplex IHC, Spatial Analysis HALO, HALO Link
Histological spatial analysis on the induction of PD-L1+ macrophages by CD8+ T cells at the marginal microenvironment of triple-negative breast cancer Suzuki K, Ohe R, Kabasawa T, Kitaoka T, Kawai M, Motoi F, Futakuchi M 2023 Breast Cancer Oncology Multiplex IHC, Spatial Analysis HALO
A neutrophil extracellular traps-related classification predicts prognosis and response to immunotherapy in colon cancer Feng C, Li Y, Tai Y, Zhang W, Wang H, Lian S, Jin-si-han E, Liu Y, Li X, Chen Q, He M, Lu Z 2023 Scientific Reports Immuno-oncology Spatial Analysis, Highplex FL, Figure Maker, TMA HALO
Specific Polo-Like Kinase 1 Expression in Nodular Lymphocyte-Predominant Hodgkin Lymphoma Suggests an Intact Immune Surveillance Program Weiss J, Gibbons K, Ehyaee V, Perez-Silos V, Zevallos A, Maienschein-Cline M, Brister E, Sverdlov M, Shah E, Balakrishna J, Symes E, Frederiksen J K, Gann P H, Post R, Lopez-Hisijos N, Reneau J, Venkataraman G, Bailey N, Brown N A, Xu M L, Murga-Zamalloa C 2023 The American Journal of Pathology Oncology Area Quantification, Spatial Analysis 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
Analysis of off-tumour toxicities of T-cell-engaging bispecific antibodies via donor-matched intestinal organoids and tumouroids Harter MF, Recaldin T, Gerard R, Avignon B, Bollen Y, Esposito C, Guja-Jarosz K, Kromer K, Filip A, Aubert J, Schneider A, Bacac M, Bscheider M, Stokar-Regenscheit N, Piscuoglio S, Beumer J, Gjorevski N 2023 Nature Biomedical Engineering Immuno-oncology Spatial Analysis, Highplex FL HALO, HALO AI
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
Targeting myeloid chemotaxis to reverse prostate cancer therapy resistance Guo C, Sharp A, Gurel B, Crespo M, Figueiredo I, Jain S, Vogl U, Rekowski J, Rouhifard M, Gallagher L, Yuan W, Carreira S, Chandran K, Paschalis A, Colombo I, Stathis A, Bertan C, Seed G, Goodall J, Raynaud F, Ruddle R, Swales K, Malia J, Bogdan D, Tiu C, Caldwell R, Aversa C, Ferreira A, Neeb A, Tunariu N, Westaby D, Carmichael J, Maza M, Yap C, Matthews R, Badham H, Prout T, Turner A, Parmar M, Tovey H, Riisnaes R, Flohr P, Gil J, Waugh D, Decordova S, Schlag A, Calì B, Alimonti A, de Bono J S 2023 Nature Oncology Spatial Analysis, Highplex FL HALO, HALO AI
Gastric tubular adenocarcinoma with diffuse neutrophils infiltrating: characteristics and probable treatment strategy Wang B, Zhu Y, Wang S, Li Z, Wang L, Rao W, Cheng N, Chen R, Ying J, Xue L 2023 Gastric Cancer Oncology Multiplex IHC, Spatial Analysis, Registration HALO
Neoadjuvant chemotherapy is linked to an amended anti-tumorigenic microenvironment in gastric cancer Huan X, Zou K, Zhang P, Ding H, Luo C, Xiang C, Xu S, Zhuang Y, Wu C, Wang Y, Wu X, Chen C, Zhang J, Yao X, Liu F, Liu S, Wu Z 2023 International Immunopharmacology Immuno-oncology Spatial Analysis, Highplex FL HALO
Analysis of off-tumour toxicities of T-cell-engaging bispecific antibodies via donor-matched intestinal organoids and tumouroids Harter MF, Recaldin T, Gerard R, Avignon B, Bollen Y, Esposito C, Guja-Jarosz K, Kromer K, Filip A, Aubert J, Schneider A, Bacac M, Bscheider M, Stokar-Regenscheit N, Piscuoglio S, Beumer J, Gjorevski N 2023 Nature Biomedical Engineering Immuno-oncology Spatial Analysis, Highplex FL HALO, HALO AI
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
Targeting myeloid chemotaxis to reverse prostate cancer therapy resistance Guo C, Sharp A, Gurel B, Crespo M, Figueiredo I, Jain S, Vogl U, Rekowski J, Rouhifard M, Gallagher L, Yuan W, Carreira S, Chandran K, Paschalis A, Colombo I, Stathis A, Bertan C, Seed G, Goodall J, Raynaud F, Ruddle R, Swales K, Malia J, Bogdan D, Tiu C, Caldwell R, Aversa C, Ferreira A, Neeb A, Tunariu N, Westaby D, Carmichael J, Maza M, Yap C, Matthews R, Badham H, Prout T, Turner A, Parmar M, Tovey H, Riisnaes R, Flohr P, Gil J, Waugh D, Decordova S, Schlag A, Calì B, Alimonti A, de Bono J S 2023 Nature Oncology Spatial Analysis, Highplex FL HALO, HALO AI
Gastric tubular adenocarcinoma with diffuse neutrophils infiltrating: characteristics and probable treatment strategy Wang B, Zhu Y, Wang S, Li Z, Wang L, Rao W, Cheng N, Chen R, Ying J, Xue L 2023 Gastric Cancer Oncology Multiplex IHC, Spatial Analysis, Registration HALO
Neoadjuvant chemotherapy is linked to an amended anti-tumorigenic microenvironment in gastric cancer Huan X, Zou K, Zhang P, Ding H, Luo C, Xiang C, Xu S, Zhuang Y, Wu C, Wang Y, Wu X, Chen C, Zhang J, Yao X, Liu F, Liu S, Wu Z 2023 International Immunopharmacology Immuno-oncology Spatial Analysis, Highplex FL HALO
Neoadjuvant radioimmunotherapy in pancreatic cancer enhances effector T cell infiltration and shortens their distances to tumor cells WANG J, GAI J, ZHANG T, NIU N, QI H, THOMAS II D L, LI K, XIA T, RODRIGUEZ C, PARKINSON R, DURHAM J, MCPHAUL T, NARANG A K, ANDERS R A, OSIPOV A, WANG H, HE J, LAHERU D A, HERMAN J M, LEE V, JAFFEE E M, THOMPSON E D, ZHU Q, ZHENG L 2024 Science Advances Immuno-oncology Spatial Analysis, Highplex FL, Registration HALO
Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis Mennillo E, Kim Y, Lee G, Rusu I, Patel R K, Dorman L C, Flynn E, Li S, Bain J L, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein M L, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho S, Beck K, El-Nachef N, Lewin S, Selvig D R, Terdiman J P, Mahadevan U, Oh D Y, Fragiadakis G K, Pisco A, Combes A J, Kattah M G 2024 Nature Communications Immunology ISH, Spatial Analysis, Highplex FL, TMA HALO, HALO AI
Serum amyloid A promotes glycolysis of neutrophils during PD-1 blockade resistance in hepatocellular carcinoma He M, Liu Y, Chen S, Deng H, Feng C, Qiao S, Chen Q, Hu Y, Chen H, Wang X, Jiang X, Xia X, Zhao M, Lyu N 2024 Nature Communications Immuno-oncology Spatial Analysis, Highplex FL HALO
PDGFRa+ ITGA11+ fibroblasts foster early-stage cancer lymphovascular invasion and lymphatic metastasis via ITGA11-SELE interplay Zheng H, An M, Luo Y, Diao X, Zhong W, Pang M, Lin Y, Chen J, Li Y, Kong Y, Zhao Y, Yin Y, Ai L, Huang J, Chen C, Lin T 2024 Cancer Cell Oncology Spatial Analysis, Highplex FL HALO
Multi-omics and imaging mass cytometry characterization of human kidneys to identify pathways and phenotypes associated with impaired kidney function. Asowata E O, Romoli S, Sargeant R, Tan J Y, Hoffmann S, Huang M M, Mahbubani K T, Krause F N, Jachimowicz D, Agren R, Koulman A, Jenkins B, Musial B, Griffin J L, Soderberg M, Ling S, Hansen P B L, Saeb-Parsy K, Woollard K J 2024 Kidney International Other ISH, Spatial Analysis, Highplex FL HALO, HALO AI
HSPA4 upregulation induces immune evasion via ALKBH5/CD58 axis in gastric cancer Suo D, Gao X, Chen Q, Zeng T, Zhan J, Li G, Zheng Y, Zhu S, Yun J, Guan XY, Li Y 2024 Journal of Experimental & Clinical Cancer Research Immuno-oncology Spatial Analysis, Highplex FL HALO
Targeting pathogenic CD8+ tissue-resident T cells with chimeric antigen receptor therapy in murine autoimmune cholangitis Zhu HX, Yang SH, Gao CY, Bian ZH, Chen XM, Huang RR, Meng QL, Li X, Jin H, Tsuneyama K, Han Y, Li L, Zhao ZB, Gershwin ME, Lian ZX 2024 Nature Communications Immunology Spatial Analysis, Highplex FL HALO
CXCL9/10-engineered dendritic cells promote T cell activation and enhance immune checkpoint blockade for lung cancer Lim R J, Salehi-Rad R, Tran M L, Oh M S, Dumitras C, Crosson W P, Li R, Patel T S, Man S, Yean C E, Abascal J, Huang Z, Ong S L, Krysan K, Dubinett S M, Liu B 2024 Cell Reports Medicine Immuno-oncology Spatial Analysis, Highplex FL HALO

Related HALO Modules

Multiplex IHC

Quantify expression of up to five brightfield stains in any cellular compartment - membrane, nucleus or cytoplasm.

Learn More
Highplex FL

Quantify expression of an unlimited number of biomarkers in any cellular compartment - membrane, nucleus or cytoplasm.

Learn More
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.

Learn More

Use the arrows above to view additional related modules

Want to Learn More?

Fill out the form below to request information about any of our software products.
You can also drop us an email at info@indicalab.com

We highly recommend using Google Chrome when filling out the form above. Please email marketing@indicalab.com for support.
Scroll to Top