Before Markup

HALO® Module

Area Quantification

Area Quantification IHC quantifies up to five brightfield stains on a per area rather than per cell or object basis. It is a flexible alternative for analyzing tissues where cell structure cannot be readily identified or where tissue area-based outputs are more reliable or meaningful measure. Area Quantification quantifies and reports stain positive area, average stain optical density for each stain, binned positivity based on optical density (0, 1+, 2+ and 3+), and area of colocalization (when multiple stains are analyzed).

Note that the Indica Labs’ Area Quantification module is included with any HALO package at no extra cost.

 

Try it out! Click here to initiate your free proof-of-concept HALO® image analysis.

File formats supported by the HALO image analysis platform:

  • Non-proprietary (JPG, TIF, OME.TIFF)
  • Nikon (ND2)
  • 3D Histech (MRXS)
  • Akoya (QPTIFF, component TIFF)
  • Olympus / Evident (VSI)
  • Hamamatsu (NDPI, NDPIS)
  • Aperio (SVS, AFI)
  • Zeiss (CZI)
  • Leica (SCN, LIF)
  • Ventana (BIF)
  • Philips (iSyntax, i2Syntax)
  • KFBIO (KFB, KFBF)
  • DICOM (DCM*)
    *whole-slide images

Publication Spotlight

The table below includes publications that cite the Area Quantification Brightfield or FL modules. 

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

TitleAuthorsYearJournalApplicationHALO ModulesProduct
Cannabinoid control of gingival immune activation in chronically SIV-infected rhesus macaques involves modulation of the indoleamine-2,3-dioxygenase-1 pathway and salivary microbiomeMcDew-White M, Lee E, Alvarez X, Sestak K, Ling B, Byrareddy S, Okeoma C, Mohan M2022EBioMedicineInfectious DiseaseArea Quantification, Cytonuclear, 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
AAV9/MFSD8 gene therapy is effective in preclinical models of neuronal ceroid lipofuscinosis type 7 diseaseChen X, Dong T, Hu Y, Shaffo F, Belur N, Mazzulli J, Gray S2022The Journal of Clinical InvestigationNeuroscienceArea Quantification, ISH/FISHHALO
Switching to Regular Diet Partially Resolves Liver Fibrosis Induced by High-Fat, High-Cholesterol Diet in MiceFarooq M, Hameed H, Dimanchi-Boitrel M, Piquet-Pellorce C, Samson M, Le Seyec J2022NutrientsMetabolismArea QuantificationHALO
High-dose rifampin improves bactericidal activity without increased intracerebral inflammation in animal models of tuberculous meningitisRuiz-Bedoya C, Mota F, Tucker E, Mahmud F, Reyes-Mantilla M, Erice C, Bahr M, Flavahan K, De Jesus P, Kim J, Foss C, Peloquin C, Hammound D, Ordonez A, Pardo C, Jain S2022The Journal of Clinical InvestigationInfectious DiseaseArea QuantificationHALO
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
The oral drug nitazoxanide restricts SARS-CoV-2 infection and attenuates disease pathogenesis in Syrian hamstersMiorin L, Mire C, Ranjbar S, Hume A, Huang J, Crossland N, White K, Laporte M, Kehrer T, Haridas V, Moreno E, Nambu A, Jangra S, Cupic A, Dejosez M, Abo K, Tseng A, Werder R, Rathnasinghe R, Mutetwa T, Ramos I, Sainz de Aja J, Garcia de Alba Rivas C, Schotsaert M, Corley R, Falvo J, Fernandez-Sesma A, Kim C, Rossingnol J, Wilson A, Zwaka T, Kotton D, Muhlberger E, Garcia-Sastre A, Goldfeld A2022bioRxivInfectious DiseaseArea QuantificationHALO
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
Extracellular vesicles released after cranial radiation: An insight into an early mechanism of brain injurySukati S, Ho J, Chaiswing L, Sompol P, Pandit H, Wei W, Izumi T, Chen Q, Weiss H, Noel T, Bondada S, Butterfield D, St. Cair D2022Brain ResearchNeuroscienceArea QuantificationHALO
An Fc-inert PD-L1◊4-1BB bispecific antibody mediates potent anti-tumor immunity in mice by combining checkpoint inhibition and conditional 4-1BB co-stimulationMuik A, Altintas I, Gieseke F, Schoedel K, Burm S, Toker A, Salcedo T, Verzijl, Eisel D, Grunwitz C, Kranz L, Vormehr M, Satijn D, Diken M, Kreiter S, Sasser K, Ahmadi T, Tureci O, Breij E, Jure-Kunkel M, Sahin U2022OncoImmunologyImmuno-oncologyArea Quantification, Immune, Multiplex IHCHALO
e The Association of Cholesterol Uptake and Synthesis with Histology and Genotype in Cortisol-Producing Adenoma (CPA)Motomura N, Yamazaki Y, Koga D, Harashima S, Gao X, Tezuka Y, Omata K, Ono Y, Morimoto R, Satoh F, Nakamura Y, Kwon G, Choi M, Ito A, Sasano H2022International Journal of Molecular SciencesArea Quantification, Cytonuclear, MembraneHALO
Collagen-VI expression is negatively mechanosensitive in pancreatic cancer cells and supports the metastatic nichePapalazarou V, Drew J, Juin A, Spence H, Nixon C, Salmeron-Sanchez M, Machesky L2022bioRxivOncologyArea Quantification, Figure MakerHALO
Transcriptional and DNA Methylation Signatures of Subcutaneous Adipose Tissue and Adipose-Derived Stem Cells in PCOS WomenDivoux A, Erdos E, Whytock K, Osborne T, Smith S2022CellsArea QuantificationHALO
Inhibition of†CK2 mitigates Alzheimerís tau pathology by†preventing NR2B synaptic mislocalizationMarshall C, McBride J, Changolkar L, Riddle D, Trojanowski J, Lee V M-Y2022Acta Neuropathologica CommunicationsArea QuantificationHALO
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
An anti-PD-1ñGITR-L bispecific agonist induces GITR clustering-mediated T cell activation for cancer immunotherapyChan S, Belmar N, Ho S, Rogers B, Stickler M, Graham M, Lee E, Tran N, Zhang D, Gupta P, Sho M, MacDonough T, Woolley A, Kim H, Zhang H, Liu W, Zheng P, Dezso Z, Halliwill K, Ceccarelli M, Rhodes S, Thakur A, Forsyth C, Xiong M, Tan S, Iyer R, Lake M, Digiammarino E, Zhou L, Bigelow L, Longenecker K, Judge R, Liu C, Trumble M, Remis J, Fox M, Cairns B, Akamatsu Y, Hollenbaugh D, Farding F, Alvarez H2022Nature CancerImmuno-oncologyArea Quantification, Cytonuclear, Highplex FLHALO
Sulforaphane exhibits antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses in vitro and in miceOrdonez A, Bullen C, Villabona-Rueda A, Thompson E, Turner M, Merino V, Yan Y, Kim J, Davis S, Komm O, Powell J, D'Alessio F, Yolken R, Jain S, Jones-Brando L2022Communications BiologyInfectious DiseaseArea Quantification, Multiplex IHCHALO
Ad26.COV2.S prevents upregulation of SARS-CoV-2 induced pathways of inflammation and thrombosis in hamsters and rhesus macaquesAid M, Vidal S, Piedra-Mora C, Ducat S, Chan C, Bondoc S, Colarusso A, Starke C, Nekorchuk M, Busman-Sahay K, Estes J, Martinot A, Barouch D2022PLOS PathogensInfectious DiseaseArea Quantification, Multiplex IHCHALO, HALO AI
Humanized mice reveal a macrophage-enriched gene signature defining human lung tissue protection during SARS-CoV-2 infectionKenney D, O'Connell A, Turcinovic J, Montanaro P, Hekman R, Tamura T, Berneshawi A, Cafiero T, Abdullatif S, Blum B, Goldstein S, Heller B, Gertje H, Bullitt E, Trachtenberg A, Chavez E, Nono E, Morrison C, Tseng A, Sheikh A, Kurnick S, Grosz K, Bosmann M, Ericsson M, Huber B, Saeed M, Balazs A, Francis K, Klose A, Paragas N, Campbell J, Connor J, Emili A, Crossland N, Ploss A, Douam F2022Cell ReportsInfectious DiseaseArea Quantification, Highplex FLHALO
Interface astrogliosis in†contact sport head impacts and†military blast exposureBabcock K, Abdolmohammadi B, Kiernan P, Mahar I, Cherry J, Alvarez V, Goldstein L, Stein T, McKee, Huber B2022Acta Neuropathologica CommunicationsNeruoscienceArea QuantificationHALO
Intraoperative abobotulinumtoxinA alleviates pain after surgery and improves general wellness in a translational animal modelCornet S, Carre D, Limana L, Castel D, Meilin S, Horn R, Pons L, Evans S, Lezmi S, Kalinichev M2022Research SquareOtherArea Quantification, Object ColocalizationHALO
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primatesRutkai I, Mayer M, Hellmers L, Ning B, Huang Z, Monjure C, Coyne C, Silvestri R, Golden N, Hensley K, Chandler K, Lehmicke G, Bix G, Maness N, Russell-Lodrigue K, Hu T, Roy C, Blair R, Bohm R, Doyle-Meyers L, Rappaport J, Fisher T2022Nature CommunicationsInfectious DiseaseArea QuantificationHALO
Hyperpolarized 13C-Pyruvate Metabolism as a Surrogate for Tumor Grade and Poor Outcome in Renal Cell CarcinomaóA Proof of Principle StudyUrsprung S, Woitek R, McLean M, Priest A, Crispin-Ortuzar M, Brodie C, Gill A, Gehrung M, Beer L, Riddick A, Field-Rayner J, Grist J, Deen S, Riemer F, Kaggie J, Zaccagna F, Duarte J, Locke M, Frary A, Aho T, Armitage J, Casey R, Mendichovszky I, Welsh S, Barrett T, Graves M, Eisen T, Mitchell T, Warren A, Brindle K, Sala E, Stewart G, Gallagher F2022CancersOncologyArea Quantification, Cytonuclear, Multiplex IHCHALO
Type I interferon regulates proteolysis by macrophages to prevent immunopathology following viral infectionLee A, Feng E, Chew M, Balint E, Poznanski S, Giles E, Zhang A, Marzok A, Revill S, Vahedi F, Dubey A, Ayaub E, Jimenez-Saiz R, McGrath J, Ritchie T, Jordana M, Jonigk D, Ackermann M, Ask K, Miller M, Richards C, Ashkar A2022PLOS PathogensInfectious DiseaseArea Quantification, Multiplex IHC, TMAHALO
Single-cell profling of†human dura and†meningioma reveals cellular meningeal landscape and†insights into†meningioma immune responseWang A, Bowman-Kirigin J, Desai R, Kang L, Patel P, Patel B, Khan S, Bender D, Marlin M, Liu J, Osbun J, Leuthardt E, Chicoine M, Dacey Jr R, Zipfel G, Kim A, DeNardo D, Petti A, Dunn G2022Genome MedicineNeuroscienceArea QuantificationHALO
Characterization and Validation of In Vitro and In Vivo Models to Investigate TNF-?-Induced Inflammation in Retinal DiseasesWeigelt C, Zippel N, Fuchs H, Rimpela A, Schonberger T, Stierstorfer B, Bakker R, Redemann N2022Translational Vision Science & TechnologyImmunology, OtherArea Quantification, Layer ThicknessHALO
An in vivo accelerated developmental myelination model for testing promyelinating therapeuticsLariosa-Willingham K, Leunoudakis D, Bragge T, Tolppanen L, Nurmi A, Flanagan M, Gibson J, Wilson D, Stratton J, Lehtimaki K, Miszczuk D2022BMC NeuroscienceNeuroscienceArea QuantificationHALO
Different types of reactions to E7386 among colorectal cancer patient?derived organoids and corresponding CAFsImai T, Naruse M, Ochiai M, Matsumoto K, Ikeda S, Kani M, Kato Y, Hirayama A, Sogo T, Hori Y, Yokoi A, Ochiai A2022Oncology LettersOncologyArea QuantificationHALO
CK2 signaling from TOLLIP-dependent perinuclear endosomes is an essential feature of†KRAS†mutant cancersBasu S, Luke B, Karim B, Martin N, Lockett S, Das S, Andresson T, Saylor K, Kozlov S, Bassel L, Esposito D, Johnson P2022bioRxivOncologyArea QuantificationHALO, HALO AI
Excessive immunosuppression by regulatory T cells antagonizes T cell response to schistosome infection in PD-1-deficient miceLu L, Li T, Feng X, Liu Z, Liu Y, Chao T, Gu Y, Huang R, Zhang F, He L, Zhou B, Kong E, Liu Z, 2022PLOS PathogensImmunology, OtherArea QuantificationHALO
Restoring Pro-healing/remodeling- associated M2a/c Macrophages using ON101 Accelerates Diabetic Wound HealingLin C, Chen C, Huang W, Chen Y, Chen S, Chou H, Hung C, Chen W, Lu C, Nian S, Chen S, Chang H, Chang V, Liu L, Kuo M, Chang S2022JID InnovationsOtherArea Quantification, CytonuclearHALO
Ginkgo Biloba Extract Reduces Cardiac and Brain Inflammation in Rats Fed a HFD and Exposed to Chronic Mental Stress through NF-?B InhibitionZhang L, Li G, Tao S, Xia P, Chaudhry N, Kaura S, Stone S, Liu M2022Mediators of InflammationImmunologyArea QuantificationHALO
ATG7 is a haploinsufficient repressor of tumor progression and promoter of metastasisLong J, Kania E, McEwan D, Barthet V, Brucoli M, Ladds M, Nossing C, Ryan K2022Proceedings of the National Academy of SciencesOncology, OtherArea QuantificationHALO
Cutaneous Lymphocyte Antigen (CLA) is a potential therapeutic target in Cutaneous T Cell LymphomaPeru S, Prochazkova-Carlotti M, Cherrier F, Velazquez J, Richard E, Idrissi Y, Cappellen D, Azzi-Martin L, Pham-Ledard A, Beylot-Barry M, Merlio J, Poglio S2022Journal of Investigative DermatologyImmuno-oncologyArea QuantificationHALO
Loss of EMP1 promotes the metastasis of human bladder cancer cells by promoting migration and conferring resistance to ferroptosis through activation of PPAR gamma signalingLiu S, Shi J, Wang L, Huang Y, Zhao B, Ding H, Liu Y, Wang W, Chen Z, Yang J2022Free Radical Biology and MedicineOncologyArea QuantificationHALO
Two independent modes of kidney stone suppression achieved by AIM/CD5L and KIM-1Matsuura K, Maehara N, Hirota A, Eguchi A, Yasuda K, Taniguchi K, Nishijima A, Matsuhashi N, Shiga Y, Ishii R, Iguchi Y, Tanabe K, Arai S, Miyazaki T2022Communications BiologyOtherArea Quantification, Figure MakerHALO
The Key Molecular Mechanisms of Sini Decoction Plus Ginseng Soup to Rescue Acute Liver Failure: Regulating PPAR? to Reduce Hepatocyte Necroptosis?He Y, Zhang Y, Zhang J, Hu X2022Journal of Inflammation ResearchOtherArea QuantificationHALO
TIE2-high cervical cancer cells promote tumor angiogenesis by upregulating TIE2 and VEGFR2 in endothelial cellsTan S, Chen Y, Du S, Li W, Liu P, Zhao J, Yang P, Cai J, Gao R, Wang Z2022Translational OncologyOncologyArea Quantification, Highplex FLHALO
The SGLT2i Dapagliflozin Reduces RV Mass Independent of Changes in RV Pressure Induced by Pulmonary Artery BandingConnelly K, Wu E, Visram A, Friedberg M, Batchu S, Yeera V, Thai K, Nghiem L, Zhang Y, Kabir G, Desjardins J, Advani A, Gilbert R2022Cardiovascular Drugs and TherapyOtherArea QuantificationHALO
The Novel Gabapentinoid Mirogabalin Prevents Upregulation of _2_-1 Subunit of Voltage-Gated Calcium Channels in Spinal Dorsal Horn in a Rat Model of Spinal Nerve LigationDomon Y, Kobayashi N, Kubota K, Kitano Y, Ueki H, Shimojo Y, Ishikawa K, Ofune Y2022Drug ResearchNeuroscienceArea QuantificationHALO
Functional Intercellular Transmission of miHTT via Extracellular Vesicles: An In Vitro Proof-of-Mechanism StudyMorais R, Sogorb-Gonzalez M, Bar C, Timmer N, Van der Bent M, Wartel M, Valles A2022CellsNeuroscienceArea QuantificationHALO
Cholesterol-Conjugated Short-Interfering RNA Silencing Tnf for the Treatment of Liver Macrophage-Mediated Acute Inflammation in Nonalcoholic Fatty Liver DiseaseCraig K, Abrams M, Amiji M2022Nucleic Acid of TherapeuticsMetabolismArea QuantificationHALO
Deep learning-based quantification of NAFLD/NASH progression in human liver biopsiesHeinemann F, Gross P, Zeveleva S, Qian H, Hill J, Hofer A, Jonigk D, Diehl A, Abdelmalek M, Lenter M, Pullen S, Guarnieri P, Stierstorfer B2022Scientific ReportsMetabolismArea QuantificationHALO, HALO AI
Glutaminase 2 Knockdown Reduces Hyperammonemia and Associated Lethality of Urea Cycle Disorder Mouse ModelMao X, Chen H, Lin A, Kim S, Burczynski M, Na E, Halasz G, Sleeman M, Murphy A, Okamoto H, Cheng X2022Journal of Inherited Metabolic DiseaseMetabolismArea Quantification, ISH/FISHHALO
What Happens to the Preserved Renal Parenchyma After Clamped Partial Nephrectomy?Xiong L, Nguyen J, Peng Y, Zhou Z, Ning K, Jia N, Nie J, Wen D, Wu Z, Roversi G, Palacios D, Abramczyk E, Munoz-Lopez C, Campbell J, Cao Y, Li Wencai, Zhang X, He Z, Li X, Huang J, Shou J, Wu J, Chen M, Chen X, Zheng J, Xu C, Zhong W, Li Z, Dong W, Zhou J, Zhang H, Luo J, Liu J, Sun G, Han H, Guo S, Dong P, Zhou F, Yu C, Campbell S, Zhang Z2022European UrologyOtherArea Quantification, ISH/FISHHALO
Defects in NLRP6, autophagy and goblet cell homeostasis are associated with reduced duodenal CRH receptor 2 expression in patients with functional dyspepsiaBruce J, Burns G, Soh W, Nair P Sherwin S, Fan K, Dowling L, Goggins B, Koloski N, Potter M, Bollipo S, Foster R, Gan L, Veysey M, Philpott D, Girardin S, Holtmann G, Kaiko G, Walker M, Talley N, Keely S2022Brain, Behavior, and ImmunityMetabolismArea QuantificationHALO
Ex vivo enzymatic treatment converts blood type A donor lungs into universal blood type lungsWang A, Ribeiro R, Ali A, Brambate E, Abdelnour-Berchtold E, Michaelsen V, Zhang Y, Rahfeld P, Moon H, Gokhale H, Gazzalle A, Pal P, Liu M, Waddell T, Cserti-Gadewich C, Tinckam K, Kizhakkedathu J, West L, Keshavjee S, Withers S, Cypel M2022Science Translational MedicineOtherArea Quantification, CytonuclearHALO
T-cell mediated targeted delivery of anti-PD-L1 nanobody overcomes poor antibody penetration and improves PD-L1 blocking at the tumor sitePierre-Florent P, Bombart R, Desimpel P, Naulaerts S, Thouvenel L, Collet J, Van den Eynde B, Zhu J2022Cancer Immunology ResearchImmuno-oncologyArea Quantification, CytonuclearHALO
Crocin alleviates cognitive impairment associated with atherosclerosis via improving neuroinflammation in LDLR_/_ mice fed a high-fat/cholesterol dietSong R, Han S, Gao H, Jiang H, Li X2022Phytotherapy ResearchNeuroscienceArea QuantificationHALO
Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal CancerRajurkar M, Parikh A, Solovyov A, You E, Kulkarni A, Chu C, Xu K, Jaicks C, Taylor M, Wu C, Alexander K, Good C, Szabolcs A, Gerstberger S, Tran A, Xu N, Ebright R, Van Seventer E, Vo K, Tai E, Lu C, Joseph-Chazan J, Raabe M, Nieman L, Desai N, Arora K, Ligorio M, Thapar V, Cohen L, Garden P, Senussi Y, Zheng H, Allen J, Blaszkowsky L, Clark J, Goyal L, Wo J, Ryan D, Cocoran R, Deshpande V, Rivera M, Aryee M, Hong T, Berger S, WAlt D, Burns K, Park P, Greenbaum B, Ting D2022Cancer DiscoveryOncologyArea Quantification, Multiplex IHCHALO
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
Atypical chemokine receptor 3 induces colorectal tumorigenesis in mice by promoting _-arrestin-NOLC1-fibrillarin-dependent rRNA biogenesisYang J, Miao R, Li Y, Pan T, Wu S, Qu X, Cui S2022Acta Pharmacologica SinicaOncologyArea QuantificationHALO
Cytotoxic granzyme C–expressing ILC1s contribute to antitumor immunity and neonatal autoimmunityNixon B, Chou C, Krishna C, Dadi S, Michel A, Cornish A, Kansler E, Do M, Wang X, Capistrano K, Rudensky A, Leslie C, Li M2022Science ImmunologyImmuno-oncologyArea QuantificationHALO
Phenotype-genotype correlation in aldosterone-producing adenomas characterized by intracellular cholesterol metabolismHarashima S, Yamazaki Y, Motomura N, Ono Y, Omata K, Tezuka Y, Morimoto R, Nakamura Y, Satoh F, Suzuki H, Kwon G, Choi M, Sasano H2022The Journal of Steroid Biochemistry and Molecular BiologyOncology, MetabolismArea Quantification, MembraneHALO
AKR1C3 regulated by NRF2/MAFG complex promotes proliferation via stabilizing PARP1 in hepatocellular carcinomaPan D, Yang W, Zeng Y, Qin H, Xu Y, Gui Y, Fan X, Tian G, Wu Y, Sun H, Ye Y, Yang S, Zhou J, Guo Q, Zhao L2022OncogeneOncologyArea Quantification, TMAHALO
Human Intestinal Myofibroblasts DepositED COLLAGEN VI EnhanceS Adhesiveness for T cells - A Novel Mechanism for Maintenance of Intestinal Inflammation.Lin S, Musso A, Wang J, Mukherjee P, West G, Mao R, Lyu R, Li J, Zhao S, Elias M, Haberman Y, Denson L, Kugathasan S, Chen M, Czarnecki D, Dejanovic D, Le H, Chandra J, Lipman J, Steele S, Nguyen Q, Fiocchi C, Rieder F2022Matrix BiologyImmunology, OtherArea QuantificationHALO
Impact of Physiologically Relevant Genistein Exposure at Different Time Windows on Puberty Onset and Neuroendocrine Function in Female RatsXiong J, Tian Y, Ma G, Wang X, Shan S, Cheng G2022Molecular Nutrition & Food ResearchOtherArea QuantificationHALO
Periostin- and podoplanin- positive cancer-associated fibroblast subtypes cooperate to shape the inflamed tumor microenvironment in aggressive pancreatic adenocarcinomaNeuzillet C, Nicolle R, Raffenne J, Tijeras-Raballand A, Brunel A, Astorgues-Xerri L, Vacher S, Arbateraz F, Fanjul M, Hilmi M, Samain R, Klein C, Perraud A, Rebours V, Mathonnet M, Bieche I, Kocher H, Cros J, Bousquet C2022Journal of PathologyOncologyArea QuantificationHALO
Gasdermin D maintains bone mass by rewiring the endo-lysosomal pathway of osteoclastic bone resorptionLi M, Yang D, Yan H, Tang Z, Jiang D, Zhang J, Chi Z, Nie W, Zhen W, Yu W, Chen S, Wang Z, Yu Q, Zhang X, Yang F, Fan S, Lin X, Wang D2022Developmental CellOtherArea Quantification, Multiplex IHCHALO
Micellar nanoparticles inhibit the postoperative inflammation, recurrence and pulmonary metastasis of 4T1 breast cancer by blocking NF-_B pathway and promoting MDSCs depletionLu Z, Ma L, Mei L, Ren K, Li M, Zhang L, Liu X, He Q2022International Journal of PharmaceuticsImmuno-oncologyArea QuantificationHALO
Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS-CoV-2Planchais C, Reyes-Ruiz A, Lacombe R, Zarantonello A, Lecerf M, Revel M, Roumenina L, Atanasov B, Mouquet H, Dimitrov J2022Protein ScienceInfectious DiseaseArea Quantification, Highplex FLHALO
Cell-specific dysregulation of iron and oxygen homeostasis as a novel pathophysiology in PSPLee S, Martinez-Valbuena I, de Andrea C, Villalba-Esparza M, Ilaalagan S, Couto B, Visanji N, Lang A, Kovacs G2022Annals of NeurologyNeuroscienceArea QuantificationHALO
The PSEN1 E280G mutation leads to increased amyloid-_43 production in induced pluripotent stem cell neurons and deposition in brain tissueWillumsen N, Arber C, Lovejoy C, Toombs J, Alatza A, Weston P, Chavez-Gutierrez L, Hardy J, Zetterberg H, Fox N, Ryan N, Lashley T, Wray S2022Brain CommunicationsNeuroscienceArea QuantificationHALO
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
URI alleviates tyrosine kinase inhibitors-induced ferroptosis by reprogramming lipid metabolism in p53 wild-type liver cancersDing Z-W, Pan Y-F, Shang T, Jiang T-Y, Lin Y-K, Yang C, Pang S, Cui X-W, Wang Y, Feng X, Xu M, Pei M, Chen Y, Li X, Ding J, Tan Y-X, Wang H, Dong L-W, Wang L2023Research SquareOncologyArea QuantificationHALO
Vascular injury is associated with repetitive head impacts and tau pathology in chronic traumatic encephalopathyKirsch D, Shah A, Dixon E, Kelley H, Cherry J, Xia W, Daley S, Aytan N, Cormier K, Kubilus C, Mathias R, Alvarez V, Huber B, McKee A, Stein T2023Journal of Neuropathology & Experimental NeurologyNeuroscienceArea QuantificationHALO
Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuationChen D-Y, Chin C, Kenney D, Tavares A, Khan N, Conway H, Liu G, Choudhary M, Gertje H, O'Connell A, Adams S, Kotton D, Herrmann A, Ensser A, Connor J, Bosmann M, Li J, Gack M, Baker S, Kirchdoerfer R, Kataria Y, Crossland N, Douam F, Saeed M2023NatureInfectious DiseaseArea QuantificationHALO
Transcriptional vulnerabilities of striatal neurons in human and rodent models of Huntington’s diseaseMatsushima A, Pineda S, Crittenden J, Lee H, Galani K, Mantero J, Tombaugh G, Kellis M, Heiman M, Graybiel A2023Nature CommunicationsNeuroscienceArea Quantification, ISH-IHC/FISH-IFHALO
Extensive and Persistent Extravascular Dermal Fibrin Deposition Characterizes Systemic SclerosisBrowning J, Bhawan J, Tseng A, Crossland N, Bujor A, Akassoglou K, Assassi S, Skaug B, Ho J2023bioRxivFibrosisArea QuantificationHALO
Butyrate alleviates cognitive impairment by improving gut mucosal barrier function and blocking neuroinflammatory signaling in LDLR -/- miceSong R, Gao H, Jiang H, Zhang W, Han S2023Research SquareNeuroscience, MetabolismArea QuantificationHALO
Inhibition of indoleamine dioxygenase leads to better control of tuberculosis adjunctive to chemotherapySingh B, Moodley C, Singh D, Escobedo R, Sharan R, Arora G, Ganatra S, Shivanna V, Gonzalez O, Hall-Ursone S, Dick Jr. E, Kaushal D, Alvarez X, Mehra S2023JCI InsightInfectious Disease, FibrosisArea Quantification, Highplex FLHALO
Altered MANF Expression in Pancreatic Acinar and Ductal Cells in Chronic Alcoholic Pancreatitis: A Cross-Sectional StudyCaldwell N, Li H, Bellizzi A, Luo J2023BiomedicinesGastroenterologyArea Quantification, CytonuclearHALO
Tau-RNA complexes inhibit microtubule polymerization and drive disease-relevant conformation changeMcMillan P, Benbow S, Uhrich R, Saxton A, Baum M, Strovas T, Wheeler J, Baker J, Liachko N, Keene C, Latimer C, Kraemer B2023BrainNeuroscienceArea QuantificationHALO
Mouse-Adapted SARS-CoV-2 MA10 Strain Displays Differential Pulmonary Tropism and Accelerated Viral Replication, Neurodissemination, and Pulmonary Host Responses in K18-hACE2 MiceThieulent C, Dittmar W, Balasuriya U, Crossland N, Wen X, Richt J, Carossino M2023mSphereInfectious DiseaseArea QuantificationHALO
Nucleolin mediates SARS-CoV-2 replication and viral-induced apoptosis of host cellsMerino V, Yan Y, Ordonez A, Bullen C, Lee A, Saeki H, Ray K, Huang T, Jain S, Pomper M2023Antiviral ResearchInfectious DiseaseArea Quantification, Multiplex IHCHALO
Genetic models of cleavage-reduced and soluble TREM2 reveal distinct effects on myelination and microglia function in the cuprizone modelBeckmann N, Neuhaus A, Zurbruegg S, volkmer P, Patino C, Joller S, Feuerbach D, Doelemeyer A, Schweizer T, Rudin S, Nuemann U, Berth R, Frieauff W, Gasparani F, Shimshek D2023Journal of NeuroinflammationNeuroscienceArea QuantificationHALO
A Comparative Study on the Distribution Pattern of Endocrine Cells in the Gastrointestinal Tract of Two Small Alpine Mammals, Plateau Zokor (Eospalax baileyi) and Plateau Pika (Ochotona curzoniae)Cai X, Bao D, Hua R, Cai B Wang L, Dong R, Hua L2023AnimalsGastroenterologyArea QuantificationHALO
Pioglitazone restores mitochondrial function but does not spare cortical tissue following mild brain contusionHubbard W, Vekaria H, Kalimon O, Spry M, Brown E, Kobaugh T, Sullivan P2023Brain CommunicationsNeuroscienceArea QuantificationHALO
Endothelial Cells are Heterogeneous in Different Brain Regions and are Dramatically Altered in Alzheimer’s DiseaseBryant A, Li Z, Jayakumar R, Serrano-Pozo A, Woost B, Hu M, Woodbury M, Wachter A, Lin G, Kwon T, Talanian R, Biber K, Karran E, Hyman B, Das S, Bennett R2023bioRxivNeuroscienceArea QuantificationHALO
Cancer-associated fibroblasts are the main contributors to epithelial-to-mesenchymal signatures in the tumor microenvironmentSzabo P, Vajdi A, Kumar N, Tolstorukov M, Chen B, Edwards R, Ligon K, Chasalow S, Chow K, Shetty A, Bolisetty M, Holloway J, Golhar R, Kidd B, Hull P, Houser J, Vlach L, Siemers N, Saha S2023Scientific ReportsOncologyArea QuantificationHALO
TGF-β in the microenvironment induces a physiologically occurring immune-suppressive senescent stateMatsuda S, Revandkar A, Dubash T, Ravi A, Wittner B, Lin M, Morris R, Burr R, Guo H, Seeger K, Szabolcs A, Che D, Nieman L, Getz G, Ting D, Lawrence M, Gainor J, Haber D, Maheswaran S2023Cell ReportsOncologyArea QuantificationHALO
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
Ubiquinone deficiency drives reverse electron transport to disrupt hepatic metabolic homeostasis in obesityGoncalves R, Wang Z, Inouye K, Lee G, Fu X, Saksi J, Rosique C, Parlakgul G, Arruda A, Hui S, Loperena M, Burgess S, Graupera I, Hotamisligil G2023bioRxivMetabolismArea QuantificationHALO
Feasibility of [18F]FSPG PET for Early Response Assessment to Combined Blockade of EGFR and Glutamine Metabolism in Wild-Type KRAS Colorectal CancerBae S, Wang J, Georgiou D, Wen X, Cohen A, Geng L, Tantawy M, Manning H2023TomographyOncologyArea QuantificationHALO
Synergistic therapeutic combination with a CAF inhibitor enhances CAR-NK-mediated cytotoxicity via reduction of CAF-released IL-6Lee Y, Go G, Koh E, Yoon H, Seo M, Hong S, Jeong J, Kim J, Cho D, Kim T, Kim S, Jun E, Jang M2023Journal for ImmunoTherapy of CancerImmuno-oncologyArea Quantification, Multiplex IHCHALO
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
Cannabinoids modulate the microbiota–gut–brain axis in HIV/SIV infection by reducing neuroinflammation and dysbiosis while concurrently elevating endocannabinoid and indole-3-propionate levelsMcDew-White M, Lee E, Premadasa L, Alvarez X, Okeoma C, Mohan M2023Journal of NeuroinflammationNeuroscience, Infectious DiseaseArea QuantificationHALO
TIPE2 Inhibits MGD Inflammation by Regulating Macrophage PolarizationZhao S, Shen Y, Wu S, Shao Y, Shi R, Yan Y, Zhao H2023Journal of Personalized MedicineImmunologyArea Quantification, Highplex FLHALO
Bi-allelic mutation in SEC16B alters collagen trafficking and increases ER stressEl-Gazzar A, Voraberger B, Rauch F, Mairhofer M, Schmidt K, Guillemyn B, Mitulovic G, Reiterer V, Haun M, Mayr M, Mayr J, Kimeswenger S, Drews O, Saraff V, Shaw N, Fratzl-Zelman N, Symoens S, Farhan H, Hogler W2023EMBO Molecular MedicineOtherArea Quantification, Highplex FLHALO
Tumour Extracellular Vesicles Induce Neutrophil Extracellular Traps To Promote Lymph Node MetastasisSu X, Brassard A, Bartolomucci A, Dhoparee-Dooma I, Qiu Q, Tsering T, Rohanizadeh R, Koufos O, Giannias B, Bourdeau F, Feng L, Leo S, Sangwan V, Tankel J, Quail D, Spicer J, Burnier J, Bailey S, Ferri L, Cools-Lartigue J2023bioRxivImmuno-oncologyArea Quantification, Highplex FLHALO
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
Sustained delivery of a heterodimer bone morphogenetic protein-2/7 via a collagen hydroxyapatite scaffold accelerates and improves critical femoral defect healingLiu Y, Puthia M, Sheehy E, Ambite I, Petrlova J, Prithviraj S, Oxborg M, Sebastian S, Vater C, Zwingenberger S, Struglics A, Bourgine P, O'Brien F, Raina D2023Acta BiomaterialiaBiomaterialsArea Quantification, Figure MakerHALO
Repertoire of P-glycoprotein drug transporters in the zoonotic nematode Toxocara canisChelladurai J, Martin K, Vardaxis P, Reinemeyer C, Vijayapalani P, Robertson A, Brewer M2023Scientific ReportsInfectious DiseaseArea QuantificationHALO
Chronic immune activation and gut barrier dysfunction is associated with neuroinflammation in ART-suppressed SIV+ rhesus macaquesByrnes S, Busman-Sahay K, Angelovich T, Younger S, Taylor-Brill S, Nekorchuk M, Bondoc S, Dannay R, Terry M, Cochrane C, Jenkins T, Roche M, Deleage C, Bosinger S, Paiardini M, Brew B, Estes J, Churchill M2023PLOS PathogensInfectious DiseaseArea Quantification, Object Colocalization, ISH, Highplex FLHALO
MAIT cell inhibition promotes liver fibrosis regression via macrophage phenotype reprogrammingMabire M, Hegde P, Hammoutene A, Wan J, Caër C, Al Sayegh R, Cadoux M, Allaire M, Weiss E, Thibault-Sogorb T, Lantz O, Goodhardt M, Paradis V, de la Grange P, Gilgenkrantz H, and Lotersztajn S2023Nature CommunicationsGastroenterologyArea QuantificationHALO
Cannabinoid enhancement of lncRNA MMP25-AS1/MMP25 interaction reduces neutrophil infiltration and intestinal epithelial injury in HIV/SIV infectionPremadasa L, Lee E, McDew-White M, Alvarez X, Jayakumar S, Ling B, Okeoma C, Byrareddy S, Kulkarni S, and Mohan M2023JCI InsightInfectious DiseaseArea Quantification, Highplex FLHALO
Disrupting the α-synuclein-ESCRT interaction with a peptide inhibitor mitigates neurodegeneration in preclinical models of Parkinson’s diseaseNim S, O'Hara D, Corbi-Verge C, Perez-Riba A, Fujisawa K, Kapadia M, Chau H, Albanese F, Pawar G, De Snoo M, Ngana S, Kim J, El-Agnaf O, Rennella E, Kay L, Kalia S, Kalia L, Kim P2023Nature CommunicationsNeuroscienceArea QuantificationHALO
In situ microwave fixation provides an instantaneous snapshot of the brain metabolomeJuras J, Webb M, Young L, Markussen K, Hawkinson T, Buoncristiani M, Bolton K, Coburn P, Williams M, Sun L, Sanders W, Bruntz R, Conroy L, Wang C, Gentry M, Smith B, Sun R2023Cell Reports MethodsOtherArea QuantificationHALO
Dual truncation of tau by caspase-2 accelerates its CHIP-mediated degradationReinhardt L, Musacchio F, Bichmann M, Behrendt A, Ercan-Herbst E, Stein J, Becher I, Haberkant P, Mader J, Schöndorf D, Schmitt M, Korffmann J, Reinhardt P, Pohl C, Savitski M, Klein C, Gasparini L, Fuhrmann M, Ehrnhoefer D2023Neurobiology of DiseaseNeuroscienceArea QuantificationHALO
Immunomodulatory amnion-derived mesenchymal stromal cells preserve muscle function in a mouse model of Duchenne muscular dystrophyNitahara-Kasahara Y, Nakayama S, Kimura K, Yamaguchi S, Kakiuchi Y, Nito C, Hayashi M, Nakaishi T, Ueda Y, Okada T2023Stem Cell Research & TherapyMyologyArea QuantificationHALO
Single cell G-protein coupled receptor profiling of activated kidney fibroblasts expressing transcription factor 21Kaur H, Yerra VG, Batchu SN, Tran DT, Kabir MDG, Liu Y, Advani SL, Sedrak P, Geldenhuys L, Tennankore KK, Poyah P, Siddiqi FS, Advani A2023British Journcal of PharmacologyFibrosisArea QuantificationHALO
Exploration of spatial heterogeneity of tumor microenvironment in nasopharyngeal carcinoma via transcriptional digital spatial profilingWang L, Wang D, Zeng X, Zhang Q, Wu H, Liu J, Wang Y, Liu G, Poan Y2023International Journal of Biological SciencesOncologyArea Quantification, ISH-IHC/FISH-IFHALO
The role of human endometrial stem cells application in endometrial-factor induced infertilityBausyte R, Vaigauskaite B, Borutinskaite V, Valatkaite E, Besusparis J, Valkiuniene R, Kazenaite E, Ramasauskaite D, Navakauskiene R2023Research SquareOtherArea QuantificationHALO
Microglial depletion does not impact alphasynuclein aggregation or nigrostriatal degeneration in the rat preformed fibril modelStoll A, Kemp C, Patterson J, Kubik M, Kuhn N, Benskey M, Duffy M, Luk K, Sortwell C2023Research SquareNeuroscienceArea QuantificationHALO
Therapeutic effects of axitinib, an anti-angiogenic tyrosine kinase inhibitor, on interstitial cystitisShin J, Ryu C, Yu H, Park Y, Shin D, Choo M2023Scientific ReportsOtherArea QuantificationHALO
Tumor-infiltrating leukocyte profiling defines three immune subtypes of NSCLC with distinct signaling pathways and genetic alterationsAoki K, Nishito Y, Motoi N, Arai Y, Hiraoka N, Shibata T, Sonobe Y, Kayukawa Y, Hashimoto E, Takahashi M, Fujii E, Nishizawa T, Fukuda H, Ohashi K, Arai K, Mizoguchi Y, Yoshida Y, Watanabe S, Yamashita M, Kitano S, Sakamoto H, Nagata Y, Mitsumori R, Ozaki K, Niida S, Kanai Y, Hirayama A, Soga T, Maruyama T, Tsukada K, Yabuki N, Shimada M, Kitazawa T, Natori O, Sawada N, Kato A, Yoshida T, Yasuda K, Mizuno H, Tsunoda H, Ochiai A2023Cancer Research CommunicationsImmuno-oncologyArea Quantification, CytonuclearHALO
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
Beta-containing bivalent SARS-CoV-2 protein vaccine elicits durable broad neutralization in macaques and protection in hamstersBerry C, Pavot V, Anosova N, Kishko M, Li L, Tibbitts T, Raillard A, Gautheron S, Cummings S, Bangari D, Kar S, Atyeo C, Deng Y, Alter G, Gutzeit C, Koutsoukos M, Chicz R, Lecouturier V2023Communications MedicineInfectious DiseaseArea QuantificationHALO
Context-dependent activation of STING-interferon signaling by CD11b agonists enhances anti-tumor immunityLiu X, Hogg G, Zuo C, Borcherding N, Baer J, Lander V, Kang LI, Knolhoff B, Ahmad F, Osterhout R, Galkin A, Bruey J, Carter L, Mpoy C, Vij K, Fields R, Schwarz J, Park H, Gupta V, DeNardo D2023Cancer CellImmuno-oncologyArea Quantification, CytonuclearHALO
Reciprocal Interaction of Cancer Stem Cells of Cholangiocarcinoma with MacrophageWang X, Golino J, Hawk N, Xie C2023Stem Cell Reviews and ReportsOncologyArea QuantificationHALO
Mucin 4 is a cellular biomarker of necrotizing bronchiolitis in influenza A virus infectionArruda B, Kanefsky R, Hau S, Janzen G, Anderson T, Baker A2023Microbes and InfectionInfectious DiseaseArea QuantificationHALO
PI3K inhibition circumvents resistance to SHP2 blockade in metastatic triple-negative breast cancerAmante RJ, Jehanno C, De Silva D, Coissieux M, Ackerknecht M, Romanet V, Sethi A, Hamelin B, Preca B, Piscuoglio S, Ng C, Mohseni M, Bentires-Alj M2023Journal of Mammary Gland Biology and NeoplasiaOncologyArea QuantificationHALO
CNS-dominant human FMRP isoform rescues seizures, fear, and sleep abnormalities in Fmr1-KO miceWong H, Hooper A, Kang H, Lee S, Zhao J, Sadhu C, Rawat S, Gray S, Hampson D2023JCI InsightNeuroscienceArea QuantificationHALO
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
Orthotopic model of pancreatic cancer using CD34+ humanized mice and generation of tumor organoids from humanized tumorsJeong J, Park S, Lee S, Kim Y, Shim I, Jeong S, Choi E, Kim J, Jun E2023International ImmunopharmacologyImmuno-oncologyArea QuantificationHALO
The Effects of Acute Ethanol Intoxication on Spinal Cord Injury Outcomes in Female MiceGlaser E, Stewart A, Jagielo-Miller J, Bailey C, Prendergast M, Gensel J2023Journal of NeurotraumaNeuroscienceArea QuantificationHALO
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
The Defenders of the Alveolus Succumb in COVID-19 Pneumonia to SARS-CoV-2 and Necroptosis, Pyroptosis and PanoptosisSchifanella L, Anderson J, Wieking G, Southern P, Antinori S, Galli M, Corbellino M, Lai A, Klatt N, Schacker T, Haase A2023The Journal of Infectious DiseaseInfectious DiseaseArea QuantificationHALO
Histological validation of atrial structural remodelling in patients with atrial fibrillationTakahashi Y, Yamaguchi T, Otsubo T, Nakashima K, Shinzato K, Osako R, Shichida S, Kawano Y, Fukui A, Kawaguchi A, Aishima S, Saito T, Takahashi N, Node K2023European Heart JournalOtherArea QuantificationHALO
Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodelingReuter MS, Sokolowski DJ, Diaz-Mejia JJ, Keunen J, de Vrijer B, Chan C, Wang L, Ryan G, Chiasson DA, Ketela T, Scherer SW, Wilson MD, Jaeggi E, and Chaturvedi RR2023Communications BiologyOtherArea QuantificationHALO
Electrical impedance myography detects dystrophin-related muscle changes in mdx miceHiyoshi T, Zhao F, Baba R, Hirakawa T, Kuboki R, Suzuki K, Tomimatsu Y, O'Donnell P, Han S, Zach N, Nakashima M2023Research SquareMyologyArea Quantification, Muscle FiberHALO
Altered expression, but small contribution, of the histone demethylase KDM6A in obstructive uropathy in miceHong LYQ, Yeung ESH, Tran DT, Yerra VGY, Kaur HK, Kabir MDG, Advani SL, Liu Y, Batchu SN, Advani A2023Disease Models & MechanismsGastroenterologyArea Quantification, Object ColocalizationHALO
Amyloid-β (Aβ) immunotherapy induced microhemorrhages are associated with activated perivascular macrophages and peripheral monocyte recruitment in Alzheimer’s disease miceTaylor X, Clark I, Fitzgerald G, Oluoch H, Hole J, DeMattos R, Wang Y, Pan F2023Molecular NeurodegenerationImmuno-oncology, NeuroscienceArea QuantificationHALO
Desialylated platelet clearance in the liver is a novel mechanism of systemic immunosuppressionLi J, Karakas D, Xue F, Chen Y, Zhu G, Ycel Y, MacParland S, Zhang H, Semple J, Freedman J, Shi Q, Ni H2023ResearchImmunologyArea QuantificationHALO
SMRT Sequencing Enables High-Throughput Identification of Novel AAVs from Capsid Shuffling and Directed EvolutionWidler Casy, Garza IT, Chen X, Dong T, Hu Y, Kanchwala M, Trygg CB, Shyng C, Xing C, Bunnell BA, Braun SE, Gray SJ2023GenesOtherArea QuantificationHALO
Differential effects of PGAM5 knockout on high fat high fructose diet and methionine choline-deficient diet induced non-alcoholic steatohepatitis (NASH) in miceLi L, Guo C, Yu Y, Tie L, Lu G, Liu F, Han X, Ji L, Zou X2023Cell & BioscienceMetabolismArea Quantification, Multiplex IHCHALO
Rosmarinic acid alleviates intestinal inflammatory damage and inhibits endoplasmic reticulum stress and smooth muscle contraction abnormalities in intestinal tissues by regulating gut microbiotaLi K, Wu J, Xu S, Li X, Zhang Y, Gao X2023Microbiology SpectrumInfectious DiseaseArea QuantificationHALO
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
Regional and cellular iron deposition patterns predict clinical subtypes of multiple system atrophyLee S, Martinez-Valbuena I, Lang AE, Kovacs GG2023Research SquareNeuroscienceArea Quantification, Object ColocalizationHALO
A novel retinoic acid receptor-γ agonist antagonizes immune checkpoint resistance in lung cancers by altering the tumor immune microenvironmentWei CH, Huang L, Kreh B, Liu X, Tyutyunyk-Massey L, Kawakami M, Chen Z, Shi M, Kozlov S, Chan KC, Andresson T, Carrington M, Vuligonda V, Sanders ME, Horowitz A, Hwu P, Peng W, Dmitrovsky E, Liu X2023Scientific ReportsImmuno-oncologyArea Quantification, CytonuclearHALO, HALO AI
Gys1 Antisense Therapy Prevents Disease-Driving Aggregates and Epileptiform Discharges in a Lafora Disease Mouse ModelDonohue K, Fitzsimmons B, Bruntz R, Markussen K, Young L, Clarke H, Coburn P, Griffith L, Sanders W, Klier J, Burke S, Maurer A, Minassian B, Sun R, Kordasiewisz H, Gentry M2023NeurotherapeuticsNeuroscienceArea QuantificationHALO
Parvalbumin in the metabolic pathway of glutamate and γ-aminobutyric acid: Influence on expression of GAD65 and GAD67Zeng C, Lei D, Lu Y, Huang Q, Wu Y, Yang S, Wu Y2023Archives of Biochemistry and BiophysicsNeuroscienceArea QuantificationHALO
A phase I, first-in-human study of TAK-164, an antibody–drug conjugate, in patients with advanced gastrointestinal cancers expressing guanylyl cyclase CKim R, Leal A, Parikh A, Ryan D, Wang S, Bahamon B, Gupta N, Moss A, Pye J, Miao H, Inguilizian H, Cleary J2023Cancer Chemotherapy and PharmacologyOncologyArea QuantificationHALO
Novel read through agent: ZKN-0013 demonstrates efficacy in APCmin model of familial adenomatous polyposisGraf M, Apte S, Terzo E, Padhye S, Shi S, Cox M, Clark R, Modur V, Badarinarayana V2023Journal of Molecular MedicineOncologyArea QuantificationHALO
p38MAPKa stromal reprogramming sensitizes metastatic breast cancer to immunotherapyFaget D, Luo X, Inkman M, Ren Q, Su X, Ding K, Waters M, Raut G, Pandey G, Dodhiawala P, Ramalho-Oliveira R, Ye J, Cole T, Murali B, Zheleznyak A, Shokeen M, Weiss K, Monahan J, DeSelm C, Lee A, Oesterreich S, Weilbaecher K, Zhang J, DeNardo D, Stewart S2023Cancer DiscoveryImmuno-oncologyArea QuantificationHALO
Vascular-Parenchymal Crosstalk Promotes Lung Fibrosis Through BMPR2 SignalingYanagihara T, Tsubouchi K, Zhou Q, Chong M, Otsubo K, Isshiki T, Schupp J, Sato S, Scallan C, Upagupta C, Revill S, Ayoub A, Chong S, Dvorkin-Gheva A, Kaminski N, Tikkanen J, Keshavjee S, Pare G, Guignabert C, Ask K, Kolb M2023American Journal of Respiratory and Critical Care MedicineFibrosisArea Quantification, ISH, TMAHALO
T cell immunotherapies engage neutrophils to eliminate tumor antigen escape variantsHirschhorn D, Budhu S, Kraehenbuehl L, Gigoux M, Schröder D, Chow A, Ricca J, Gasmi B, De Henau O, Mangarin L, Li Y, Hamadene L, Flamar A, Choi H, Cortez C, Liu C, Holland A, Schad S, Schulze I, Warner A, Hollmann T, Arora A, Panageas K, Rizzuto G, Duhen R, Weinberg A, Spencer C, Ng D, He X, Albrengues J, Redmond D, Egeblad M, Wolchok J, Merghoub T2023CellArea Quantification, Highplex FLHALO
Coptisine modulates the pharmacokinetics of florfenicol by targeting CYP1A2, CYP2C11 and CYP3A1 in the liver and P-gp in the jejunum of rats: a pilot studyLi S, Zhang M, Wang B, Li X, Liang G2023XenobioticaGastroenterologyArea QuantificationHALO
Phase I Study of SYNB1891, an Engineered E. coli Nissle Strain Expressing STING Agonist, with and without Atezolizumab in Advanced MalignanciesLuke J, Piha-Paul S, Medina T, Verschraegen C, Varterasian M, Brennan A, Rise R, Sokolovska A, Strauss J, Hava D, Janku F2023Clinical Cancer ResearchImmuno-oncologyArea Quantification
Hepatic proinflammatory myeloid phenotypes are a hallmark of Ebola virus Kikwit pathogenesis in rhesus monkeysTseng A, Carossino M, Gertje H, O'Connell A, Gummuluru S, Kolachalama V, Balasuriya U, Connor J, Bennett R, Liu D, Hensley L, Crossland N2023Veterinary PathologyInfectious DiseaseArea Quantification, Highplex FLHALO
Nicotinamide N-methyltransferase sustains a core epigenetic program that promotes metastatic colonization in breast cancerPinto Couto J, Vulin M, Jehanno C, Coissieux M, Hamelin B, Schmidt A, Ivanek R, Sethi A, Bräutigam K, Frei A, Hager C, Manivannan M, Gómez-Miragaya J, Obradović M, Varga Z, Koelzer V, Mertz K, Bentires-Alj M2023The EMBO JournalOncologyArea Quantification, Multiplex IHCHALO, HALO AI
Effect of Dupilumab on Type 2 Biomarkers in Chronic Rhinosinusitis With Nasal Polyps: SINUS-52 Study ResultsBachert C, Laidlaw T, Cho S, Mullol J, Swanson B, Naimi S, Classe M, Harel S, Jagerschmidt A, Laws E, Ruddy M, Praestgaard A, Amin N, Mannent L2023Annals of Otology, Rhinology & LaryngologyOtherArea QuantificationHALO, HALO AI
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
ASK1 inhibitors are potential pan-antiviral drugs, which dampen replication of diverse viruses including SARS-CoV2Demian W, Jacob R, Cormier O, Nazli A, Melki M, Asavajaru A, Baid K, Zhang A, Miller M, Kaushic C, Banerjee A, Mossman K2023Antiviral ResearchInfectious DiseaseArea QuantificationHALO
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
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

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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