Simultaneously analyze an unlimited number of fluorescent dyes on a per-area basis with the HALO® Area Quantification FL module. This flexible module provides an alternative for analyzing tissues where cell structure cannot be easily identified or where tissue area-based outputs are a more reliable or meaningful measure. Take your area-based analysis to the next level with quantification of dye positive area, average intensity, and binned positivity by intensity. After analysis, leverage interactive markups to dynamically explore dye colocalization.
Indica Labs’ Area Quantification FL module is included with every 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
Quantitative RNAscope Image Analysis Guide
From experimental design considerations to optimized setup of HALO image analysis parameters, our guide will help take your quantitative RNAscope™ image analysis to the next level.
Optimizing quantitative analysis of highly multiplexed CODEX images in HALO
31 March 2022 | In this webinar, Dr. Noemi Kedei, a staff scientist at the Collaborative Protein Technology Resource core of the Center for Cancer
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!
| Title | Authors | Year | Journal | Application | HALO Modules | Product |
|---|---|---|---|---|---|---|
| Cannabinoid control of gingival immune activation in chronically SIV-infected rhesus macaques involves modulation of the indoleamine-2,3-dioxygenase-1 pathway and salivary microbiome | McDew-White M, Lee E, Alvarez X, Sestak K, Ling B, Byrareddy S, Okeoma C, Mohan M | 2022 | EBioMedicine | Infectious Disease | Area Quantification, Cytonuclear, 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 |
| AAV9/MFSD8 gene therapy is effective in preclinical models of neuronal ceroid lipofuscinosis type 7 disease | Chen X, Dong T, Hu Y, Shaffo F, Belur N, Mazzulli J, Gray S | 2022 | The Journal of Clinical Investigation | Neuroscience | Area Quantification, ISH/FISH | HALO |
| Switching to Regular Diet Partially Resolves Liver Fibrosis Induced by High-Fat, High-Cholesterol Diet in Mice | Farooq M, Hameed H, Dimanchi-Boitrel M, Piquet-Pellorce C, Samson M, Le Seyec J | 2022 | Nutrients | Metabolism | Area Quantification | HALO |
| High-dose rifampin improves bactericidal activity without increased intracerebral inflammation in animal models of tuberculous meningitis | Ruiz-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 S | 2022 | The Journal of Clinical Investigation | Infectious Disease | Area Quantification | HALO |
| Therapeutic treatment with the anti-inflammatory drug candidate MW151 may partially reduce memory impairment and normalizes hippocampal metabolic markers in a mouse model of comorbid amyloid and vascular pathology | Braun D, Powell D, McLouth C, Roy S, Watterson D, Van Eldik | 2022 | PLOS One | Neruoscience | Classifier, Area Quantification | HALO |
| The oral drug nitazoxanide restricts SARS-CoV-2 infection and attenuates disease pathogenesis in Syrian hamsters | Miorin 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 A | 2022 | bioRxiv | Infectious Disease | Area Quantification | HALO |
| Pancreas resident macrophage-induced fibrosis has divergent roles in pancreas inflammatory injury and PDAC | Baer J, Zuo C, Kang L, Alarcon de la Lastra A, Bocherding N, Knolhoff B, Bogner S, Zhu Y, Lewis M, Zhang N, Kim K, Fields R, Mills J, Ding L, Randolph G, DeNardo D | 2022 | bioRxiv | Fibrosis | Classifier, Area Quantification, Cytonuclear, Multiplex IHC, Highplex FL, Figure Maker | HALO |
| Extracellular vesicles released after cranial radiation: An insight into an early mechanism of brain injury | Sukati 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 D | 2022 | Brain Research | Neuroscience | Area Quantification | HALO |
| 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-stimulation | Muik 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 U | 2022 | OncoImmunology | Immuno-oncology | Area Quantification, Immune, Multiplex IHC | HALO |
| 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 H | 2022 | International Journal of Molecular Sciences | Area Quantification, Cytonuclear, Membrane | HALO | |
| Collagen-VI expression is negatively mechanosensitive in pancreatic cancer cells and supports the metastatic niche | Papalazarou V, Drew J, Juin A, Spence H, Nixon C, Salmeron-Sanchez M, Machesky L | 2022 | bioRxiv | Oncology | Area Quantification, Figure Maker | HALO |
| Transcriptional and DNA Methylation Signatures of Subcutaneous Adipose Tissue and Adipose-Derived Stem Cells in PCOS Women | Divoux A, Erdos E, Whytock K, Osborne T, Smith S | 2022 | Cells | Area Quantification | HALO | |
| Inhibition of†CK2 mitigates Alzheimerís tau pathology by†preventing NR2B synaptic mislocalization | Marshall C, McBride J, Changolkar L, Riddle D, Trojanowski J, Lee V M-Y | 2022 | Acta Neuropathologica Communications | Area Quantification | HALO | |
| Fatal Neurodissemination and SARS-CoV-2 Tropism in K18-hACE2 Mice Is Only Partially Dependent on hACE2 Expression | Carossino M, Kenney D, O'Connell A, Montarnaro P, Tseng A, Gertje H, Grosz K, Ericsson M, Huber B, Kurnick S, Subramaniam S, Kirkland T, Walker J, Francis K, Klose A, Paragas N, Bosmann M, Saeed M, Balasuriya U, Douam F, Crossland N | 2022 | Viruses | Infectious Disease | Classifier, Area Quantification, Highplex FL | HALO |
| An anti-PD-1ñGITR-L bispecific agonist induces GITR clustering-mediated T cell activation for cancer immunotherapy | Chan 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 H | 2022 | Nature Cancer | Immuno-oncology | Area Quantification, Cytonuclear, Highplex FL | HALO |
| Sulforaphane exhibits antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses in vitro and in mice | Ordonez 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 L | 2022 | Communications Biology | Infectious Disease | Area Quantification, Multiplex IHC | HALO |
| Ad26.COV2.S prevents upregulation of SARS-CoV-2 induced pathways of inflammation and thrombosis in hamsters and rhesus macaques | Aid 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 D | 2022 | PLOS Pathogens | Infectious Disease | Area Quantification, Multiplex IHC | HALO, HALO AI |
| Humanized mice reveal a macrophage-enriched gene signature defining human lung tissue protection during SARS-CoV-2 infection | Kenney 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 F | 2022 | Cell Reports | Infectious Disease | Area Quantification, Highplex FL | HALO |
| Interface astrogliosis in†contact sport head impacts and†military blast exposure | Babcock K, Abdolmohammadi B, Kiernan P, Mahar I, Cherry J, Alvarez V, Goldstein L, Stein T, McKee, Huber B | 2022 | Acta Neuropathologica Communications | Neruoscience | Area Quantification | HALO |
| Intraoperative abobotulinumtoxinA alleviates pain after surgery and improves general wellness in a translational animal model | Cornet S, Carre D, Limana L, Castel D, Meilin S, Horn R, Pons L, Evans S, Lezmi S, Kalinichev M | 2022 | Research Square | Other | Area Quantification, Object Colocalization | HALO |
| Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates | Rutkai 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 T | 2022 | Nature Communications | Infectious Disease | Area Quantification | HALO |
| Hyperpolarized 13C-Pyruvate Metabolism as a Surrogate for Tumor Grade and Poor Outcome in Renal Cell CarcinomaóA Proof of Principle Study | Ursprung 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 F | 2022 | Cancers | Oncology | Area Quantification, Cytonuclear, Multiplex IHC | HALO |
| Type I interferon regulates proteolysis by macrophages to prevent immunopathology following viral infection | Lee 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 A | 2022 | PLOS Pathogens | Infectious Disease | Area Quantification, Multiplex IHC, TMA | HALO |
| Single-cell profling of†human dura and†meningioma reveals cellular meningeal landscape and†insights into†meningioma immune response | Wang 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 G | 2022 | Genome Medicine | Neuroscience | Area Quantification | HALO |
| Characterization and Validation of In Vitro and In Vivo Models to Investigate TNF-?-Induced Inflammation in Retinal Diseases | Weigelt C, Zippel N, Fuchs H, Rimpela A, Schonberger T, Stierstorfer B, Bakker R, Redemann N | 2022 | Translational Vision Science & Technology | Immunology, Other | Area Quantification, Layer Thickness | HALO |
| An in vivo accelerated developmental myelination model for testing promyelinating therapeutics | Lariosa-Willingham K, Leunoudakis D, Bragge T, Tolppanen L, Nurmi A, Flanagan M, Gibson J, Wilson D, Stratton J, Lehtimaki K, Miszczuk D | 2022 | BMC Neuroscience | Neuroscience | Area Quantification | HALO |
| Different types of reactions to E7386 among colorectal cancer patient?derived organoids and corresponding CAFs | Imai T, Naruse M, Ochiai M, Matsumoto K, Ikeda S, Kani M, Kato Y, Hirayama A, Sogo T, Hori Y, Yokoi A, Ochiai A | 2022 | Oncology Letters | Oncology | Area Quantification | HALO |
| CK2 signaling from TOLLIP-dependent perinuclear endosomes is an essential feature of†KRAS†mutant cancers | Basu S, Luke B, Karim B, Martin N, Lockett S, Das S, Andresson T, Saylor K, Kozlov S, Bassel L, Esposito D, Johnson P | 2022 | bioRxiv | Oncology | Area Quantification | HALO, HALO AI |
| Excessive immunosuppression by regulatory T cells antagonizes T cell response to schistosome infection in PD-1-deficient mice | Lu 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, | 2022 | PLOS Pathogens | Immunology, Other | Area Quantification | HALO |
| Restoring Pro-healing/remodeling- associated M2a/c Macrophages using ON101 Accelerates Diabetic Wound Healing | Lin 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 S | 2022 | JID Innovations | Other | Area Quantification, Cytonuclear | HALO |
| Ginkgo Biloba Extract Reduces Cardiac and Brain Inflammation in Rats Fed a HFD and Exposed to Chronic Mental Stress through NF-?B Inhibition | Zhang L, Li G, Tao S, Xia P, Chaudhry N, Kaura S, Stone S, Liu M | 2022 | Mediators of Inflammation | Immunology | Area Quantification | HALO |
| ATG7 is a haploinsufficient repressor of tumor progression and promoter of metastasis | Long J, Kania E, McEwan D, Barthet V, Brucoli M, Ladds M, Nossing C, Ryan K | 2022 | Proceedings of the National Academy of Sciences | Oncology, Other | Area Quantification | HALO |
| Cutaneous Lymphocyte Antigen (CLA) is a potential therapeutic target in Cutaneous T Cell Lymphoma | Peru 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 S | 2022 | Journal of Investigative Dermatology | Immuno-oncology | Area Quantification | HALO |
| Loss of EMP1 promotes the metastasis of human bladder cancer cells by promoting migration and conferring resistance to ferroptosis through activation of PPAR gamma signaling | Liu S, Shi J, Wang L, Huang Y, Zhao B, Ding H, Liu Y, Wang W, Chen Z, Yang J | 2022 | Free Radical Biology and Medicine | Oncology | Area Quantification | HALO |
| Two independent modes of kidney stone suppression achieved by AIM/CD5L and KIM-1 | Matsuura 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 T | 2022 | Communications Biology | Other | Area Quantification, Figure Maker | HALO |
| 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 X | 2022 | Journal of Inflammation Research | Other | Area Quantification | HALO |
| TIE2-high cervical cancer cells promote tumor angiogenesis by upregulating TIE2 and VEGFR2 in endothelial cells | Tan S, Chen Y, Du S, Li W, Liu P, Zhao J, Yang P, Cai J, Gao R, Wang Z | 2022 | Translational Oncology | Oncology | Area Quantification, Highplex FL | HALO |
| The SGLT2i Dapagliflozin Reduces RV Mass Independent of Changes in RV Pressure Induced by Pulmonary Artery Banding | Connelly K, Wu E, Visram A, Friedberg M, Batchu S, Yeera V, Thai K, Nghiem L, Zhang Y, Kabir G, Desjardins J, Advani A, Gilbert R | 2022 | Cardiovascular Drugs and Therapy | Other | Area Quantification | HALO |
| 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 Ligation | Domon Y, Kobayashi N, Kubota K, Kitano Y, Ueki H, Shimojo Y, Ishikawa K, Ofune Y | 2022 | Drug Research | Neuroscience | Area Quantification | HALO |
| Functional Intercellular Transmission of miHTT via Extracellular Vesicles: An In Vitro Proof-of-Mechanism Study | Morais R, Sogorb-Gonzalez M, Bar C, Timmer N, Van der Bent M, Wartel M, Valles A | 2022 | Cells | Neuroscience | Area Quantification | HALO |
| Cholesterol-Conjugated Short-Interfering RNA Silencing Tnf for the Treatment of Liver Macrophage-Mediated Acute Inflammation in Nonalcoholic Fatty Liver Disease | Craig K, Abrams M, Amiji M | 2022 | Nucleic Acid of Therapeutics | Metabolism | Area Quantification | HALO |
| Deep learning-based quantification of NAFLD/NASH progression in human liver biopsies | Heinemann F, Gross P, Zeveleva S, Qian H, Hill J, Hofer A, Jonigk D, Diehl A, Abdelmalek M, Lenter M, Pullen S, Guarnieri P, Stierstorfer B | 2022 | Scientific Reports | Metabolism | Area Quantification | HALO, HALO AI |
| Glutaminase 2 Knockdown Reduces Hyperammonemia and Associated Lethality of Urea Cycle Disorder Mouse Model | Mao X, Chen H, Lin A, Kim S, Burczynski M, Na E, Halasz G, Sleeman M, Murphy A, Okamoto H, Cheng X | 2022 | Journal of Inherited Metabolic Disease | Metabolism | Area Quantification, ISH/FISH | HALO |
| 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 Z | 2022 | European Urology | Other | Area Quantification, ISH/FISH | HALO |
| Defects in NLRP6, autophagy and goblet cell homeostasis are associated with reduced duodenal CRH receptor 2 expression in patients with functional dyspepsia | Bruce 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 S | 2022 | Brain, Behavior, and Immunity | Metabolism | Area Quantification | HALO |
| Ex vivo enzymatic treatment converts blood type A donor lungs into universal blood type lungs | Wang 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 M | 2022 | Science Translational Medicine | Other | Area Quantification, Cytonuclear | HALO |
| T-cell mediated targeted delivery of anti-PD-L1 nanobody overcomes poor antibody penetration and improves PD-L1 blocking at the tumor site | Pierre-Florent P, Bombart R, Desimpel P, Naulaerts S, Thouvenel L, Collet J, Van den Eynde B, Zhu J | 2022 | Cancer Immunology Research | Immuno-oncology | Area Quantification, Cytonuclear | HALO |
| Crocin alleviates cognitive impairment associated with atherosclerosis via improving neuroinflammation in LDLR_/_ mice fed a high-fat/cholesterol diet | Song R, Han S, Gao H, Jiang H, Li X | 2022 | Phytotherapy Research | Neuroscience | Area Quantification | HALO |
| Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer | Rajurkar 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 D | 2022 | Cancer Discovery | Oncology | Area Quantification, Multiplex IHC | HALO |
| Inflammatory Monocytes Promote Granuloma-Mediated Control of Persistent Salmonella Infection | Bettke J, Tam J, Montoya V, Butler B, vander Velden A | 2022 | Infection and Immunity | Infectious Disease | Classifier, Area Quantification | HALO |
| Atypical chemokine receptor 3 induces colorectal tumorigenesis in mice by promoting _-arrestin-NOLC1-fibrillarin-dependent rRNA biogenesis | Yang J, Miao R, Li Y, Pan T, Wu S, Qu X, Cui S | 2022 | Acta Pharmacologica Sinica | Oncology | Area Quantification | HALO |
| Cytotoxic granzyme C–expressing ILC1s contribute to antitumor immunity and neonatal autoimmunity | Nixon B, Chou C, Krishna C, Dadi S, Michel A, Cornish A, Kansler E, Do M, Wang X, Capistrano K, Rudensky A, Leslie C, Li M | 2022 | Science Immunology | Immuno-oncology | Area Quantification | HALO |
| Phenotype-genotype correlation in aldosterone-producing adenomas characterized by intracellular cholesterol metabolism | Harashima S, Yamazaki Y, Motomura N, Ono Y, Omata K, Tezuka Y, Morimoto R, Nakamura Y, Satoh F, Suzuki H, Kwon G, Choi M, Sasano H | 2022 | The Journal of Steroid Biochemistry and Molecular Biology | Oncology, Metabolism | Area Quantification, Membrane | HALO |
| AKR1C3 regulated by NRF2/MAFG complex promotes proliferation via stabilizing PARP1 in hepatocellular carcinoma | Pan 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 L | 2022 | Oncogene | Oncology | Area Quantification, TMA | HALO |
| 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 F | 2022 | Matrix Biology | Immunology, Other | Area Quantification | HALO |
| Impact of Physiologically Relevant Genistein Exposure at Different Time Windows on Puberty Onset and Neuroendocrine Function in Female Rats | Xiong J, Tian Y, Ma G, Wang X, Shan S, Cheng G | 2022 | Molecular Nutrition & Food Research | Other | Area Quantification | HALO |
| Periostin- and podoplanin- positive cancer-associated fibroblast subtypes cooperate to shape the inflamed tumor microenvironment in aggressive pancreatic adenocarcinoma | Neuzillet 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 C | 2022 | Journal of Pathology | Oncology | Area Quantification | HALO |
| Gasdermin D maintains bone mass by rewiring the endo-lysosomal pathway of osteoclastic bone resorption | Li 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 D | 2022 | Developmental Cell | Other | Area Quantification, Multiplex IHC | HALO |
| Micellar nanoparticles inhibit the postoperative inflammation, recurrence and pulmonary metastasis of 4T1 breast cancer by blocking NF-_B pathway and promoting MDSCs depletion | Lu Z, Ma L, Mei L, Ren K, Li M, Zhang L, Liu X, He Q | 2022 | International Journal of Pharmaceutics | Immuno-oncology | Area Quantification | HALO |
| Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS-CoV-2 | Planchais C, Reyes-Ruiz A, Lacombe R, Zarantonello A, Lecerf M, Revel M, Roumenina L, Atanasov B, Mouquet H, Dimitrov J | 2022 | Protein Science | Infectious Disease | Area Quantification, Highplex FL | HALO |
| Cell-specific dysregulation of iron and oxygen homeostasis as a novel pathophysiology in PSP | Lee S, Martinez-Valbuena I, de Andrea C, Villalba-Esparza M, Ilaalagan S, Couto B, Visanji N, Lang A, Kovacs G | 2022 | Annals of Neurology | Neuroscience | Area Quantification | HALO |
| The PSEN1 E280G mutation leads to increased amyloid-_43 production in induced pluripotent stem cell neurons and deposition in brain tissue | Willumsen 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 S | 2022 | Brain Communications | Neuroscience | Area Quantification | HALO |
| Innate immune receptor C5aR1 regulates cancer cell fate and can be targeted to improve radiotherapy in tumours with immunosuppressive microenvironments | Beach C, MacLean D, Majorova D, Melemenidis S, Nambiar D, Kim R, Valbuena G, Guglietta S, Krieg C, Darvish D, Suwa T, Eason A, Domingo E, Moon E, Jiang D, Jiang Y, Koong A, Woodruff T, Graves E, Maughan T, Buczacki S, Stucki M, Le Q-T, Leedham S, Giaccia A, Olcina M | 2023 | bioRxiv | Immuno-oncology | Classifier, Area Quantification, Highplex FL | HALO |
| URI alleviates tyrosine kinase inhibitors-induced ferroptosis by reprogramming lipid metabolism in p53 wild-type liver cancers | Ding 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 L | 2023 | Research Square | Oncology | Area Quantification | HALO |
| Vascular injury is associated with repetitive head impacts and tau pathology in chronic traumatic encephalopathy | Kirsch 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 T | 2023 | Journal of Neuropathology & Experimental Neurology | Neuroscience | Area Quantification | HALO |
| Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation | Chen 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 M | 2023 | Nature | Infectious Disease | Area Quantification | HALO |
| Transcriptional vulnerabilities of striatal neurons in human and rodent models of Huntington’s disease | Matsushima A, Pineda S, Crittenden J, Lee H, Galani K, Mantero J, Tombaugh G, Kellis M, Heiman M, Graybiel A | 2023 | Nature Communications | Neuroscience | Area Quantification, ISH-IHC/FISH-IF | HALO |
| Extensive and Persistent Extravascular Dermal Fibrin Deposition Characterizes Systemic Sclerosis | Browning J, Bhawan J, Tseng A, Crossland N, Bujor A, Akassoglou K, Assassi S, Skaug B, Ho J | 2023 | bioRxiv | Fibrosis | Area Quantification | HALO |
| Butyrate alleviates cognitive impairment by improving gut mucosal barrier function and blocking neuroinflammatory signaling in LDLR -/- mice | Song R, Gao H, Jiang H, Zhang W, Han S | 2023 | Research Square | Neuroscience, Metabolism | Area Quantification | HALO |
| Inhibition of indoleamine dioxygenase leads to better control of tuberculosis adjunctive to chemotherapy | Singh 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 S | 2023 | JCI Insight | Infectious Disease, Fibrosis | Area Quantification, Highplex FL | HALO |
| Altered MANF Expression in Pancreatic Acinar and Ductal Cells in Chronic Alcoholic Pancreatitis: A Cross-Sectional Study | Caldwell N, Li H, Bellizzi A, Luo J | 2023 | Biomedicines | Gastroenterology | Area Quantification, Cytonuclear | HALO |
| Tau-RNA complexes inhibit microtubule polymerization and drive disease-relevant conformation change | McMillan P, Benbow S, Uhrich R, Saxton A, Baum M, Strovas T, Wheeler J, Baker J, Liachko N, Keene C, Latimer C, Kraemer B | 2023 | Brain | Neuroscience | Area Quantification | HALO |
| Mouse-Adapted SARS-CoV-2 MA10 Strain Displays Differential Pulmonary Tropism and Accelerated Viral Replication, Neurodissemination, and Pulmonary Host Responses in K18-hACE2 Mice | Thieulent C, Dittmar W, Balasuriya U, Crossland N, Wen X, Richt J, Carossino M | 2023 | mSphere | Infectious Disease | Area Quantification | HALO |
| Nucleolin mediates SARS-CoV-2 replication and viral-induced apoptosis of host cells | Merino V, Yan Y, Ordonez A, Bullen C, Lee A, Saeki H, Ray K, Huang T, Jain S, Pomper M | 2023 | Antiviral Research | Infectious Disease | Area Quantification, Multiplex IHC | HALO |
| Genetic models of cleavage-reduced and soluble TREM2 reveal distinct effects on myelination and microglia function in the cuprizone model | Beckmann 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 D | 2023 | Journal of Neuroinflammation | Neuroscience | Area Quantification | HALO |
| 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 L | 2023 | Animals | Gastroenterology | Area Quantification | HALO |
| Pioglitazone restores mitochondrial function but does not spare cortical tissue following mild brain contusion | Hubbard W, Vekaria H, Kalimon O, Spry M, Brown E, Kobaugh T, Sullivan P | 2023 | Brain Communications | Neuroscience | Area Quantification | HALO |
| Endothelial Cells are Heterogeneous in Different Brain Regions and are Dramatically Altered in Alzheimer’s Disease | Bryant 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 R | 2023 | bioRxiv | Neuroscience | Area Quantification | HALO |
| Cancer-associated fibroblasts are the main contributors to epithelial-to-mesenchymal signatures in the tumor microenvironment | Szabo 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 S | 2023 | Scientific Reports | Oncology | Area Quantification | HALO |
| TGF-β in the microenvironment induces a physiologically occurring immune-suppressive senescent state | Matsuda 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 S | 2023 | Cell Reports | Oncology | Area Quantification | HALO |
| MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progression | Chen J, Zheng Q, Hicks J, Trabzonlu L, Ozbek B, Jones T, Vaghasia A, Larman T, Wang R, Markowski M, Denmeade S, Pienta K, Hruban R, Antonaraskis E, Gupta A, Dang C, Yegnasubramanian S, De Marzo A | 2023 | bioRxiv | Oncology | Classifier, Area Quantification | HALO |
| Ubiquinone deficiency drives reverse electron transport to disrupt hepatic metabolic homeostasis in obesity | Goncalves 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 G | 2023 | bioRxiv | Metabolism | Area Quantification | HALO |
| Feasibility of [18F]FSPG PET for Early Response Assessment to Combined Blockade of EGFR and Glutamine Metabolism in Wild-Type KRAS Colorectal Cancer | Bae S, Wang J, Georgiou D, Wen X, Cohen A, Geng L, Tantawy M, Manning H | 2023 | Tomography | Oncology | Area Quantification | HALO |
| Synergistic therapeutic combination with a CAF inhibitor enhances CAR-NK-mediated cytotoxicity via reduction of CAF-released IL-6 | Lee Y, Go G, Koh E, Yoon H, Seo M, Hong S, Jeong J, Kim J, Cho D, Kim T, Kim S, Jun E, Jang M | 2023 | Journal for ImmunoTherapy of Cancer | Immuno-oncology | Area Quantification, Multiplex IHC | HALO |
| Myeloid-specific deletion of activating transcription factor 6 alpha increases CD11b+ macrophage subpopulations and aggravates lung fibrosis | Mekhael O, Revill S, Hayat A, Cass S, MacDonald K, Vierhout M, Ayoub A, Reihani A, Padwal M, Imani J, Ayaub E, Yousof T, Dvorkin-Gheva A, Rullo A, Hirota J, Richards C, Bridgewater D, Stämpfli M, Hambly N, Naqvi A, Kolb M, Ask K | 2023 | Immunology and Cell Biology | Immunology, Fibrosis | Classifier, Area Quantification, FISH, Multiplex IHC | HALO |
| Cannabinoids modulate the microbiota–gut–brain axis in HIV/SIV infection by reducing neuroinflammation and dysbiosis while concurrently elevating endocannabinoid and indole-3-propionate levels | McDew-White M, Lee E, Premadasa L, Alvarez X, Okeoma C, Mohan M | 2023 | Journal of Neuroinflammation | Neuroscience, Infectious Disease | Area Quantification | HALO |
| TIPE2 Inhibits MGD Inflammation by Regulating Macrophage Polarization | Zhao S, Shen Y, Wu S, Shao Y, Shi R, Yan Y, Zhao H | 2023 | Journal of Personalized Medicine | Immunology | Area Quantification, Highplex FL | HALO |
| Bi-allelic mutation in SEC16B alters collagen trafficking and increases ER stress | El-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 W | 2023 | EMBO Molecular Medicine | Other | Area Quantification, Highplex FL | HALO |
| Tumour Extracellular Vesicles Induce Neutrophil Extracellular Traps To Promote Lymph Node Metastasis | Su 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 J | 2023 | bioRxiv | Immuno-oncology | Area Quantification, Highplex FL | 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 | |
| Sustained delivery of a heterodimer bone morphogenetic protein-2/7 via a collagen hydroxyapatite scaffold accelerates and improves critical femoral defect healing | Liu 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 D | 2023 | Acta Biomaterialia | Biomaterials | Area Quantification, Figure Maker | HALO |
| Repertoire of P-glycoprotein drug transporters in the zoonotic nematode Toxocara canis | Chelladurai J, Martin K, Vardaxis P, Reinemeyer C, Vijayapalani P, Robertson A, Brewer M | 2023 | Scientific Reports | Infectious Disease | Area Quantification | HALO |
| Chronic immune activation and gut barrier dysfunction is associated with neuroinflammation in ART-suppressed SIV+ rhesus macaques | Byrnes 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 M | 2023 | PLOS Pathogens | Infectious Disease | Area Quantification, Object Colocalization, ISH, Highplex FL | HALO |
| MAIT cell inhibition promotes liver fibrosis regression via macrophage phenotype reprogramming | Mabire 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 S | 2023 | Nature Communications | Gastroenterology | Area Quantification | HALO |
| Cannabinoid enhancement of lncRNA MMP25-AS1/MMP25 interaction reduces neutrophil infiltration and intestinal epithelial injury in HIV/SIV infection | Premadasa L, Lee E, McDew-White M, Alvarez X, Jayakumar S, Ling B, Okeoma C, Byrareddy S, Kulkarni S, and Mohan M | 2023 | JCI Insight | Infectious Disease | Area Quantification, Highplex FL | HALO |
| Disrupting the α-synuclein-ESCRT interaction with a peptide inhibitor mitigates neurodegeneration in preclinical models of Parkinson’s disease | Nim 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 P | 2023 | Nature Communications | Neuroscience | Area Quantification | HALO |
| In situ microwave fixation provides an instantaneous snapshot of the brain metabolome | Juras 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 R | 2023 | Cell Reports Methods | Other | Area Quantification | HALO |
| Dual truncation of tau by caspase-2 accelerates its CHIP-mediated degradation | Reinhardt 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 D | 2023 | Neurobiology of Disease | Neuroscience | Area Quantification | HALO |
| Immunomodulatory amnion-derived mesenchymal stromal cells preserve muscle function in a mouse model of Duchenne muscular dystrophy | Nitahara-Kasahara Y, Nakayama S, Kimura K, Yamaguchi S, Kakiuchi Y, Nito C, Hayashi M, Nakaishi T, Ueda Y, Okada T | 2023 | Stem Cell Research & Therapy | Myology | Area Quantification | HALO |
| Single cell G-protein coupled receptor profiling of activated kidney fibroblasts expressing transcription factor 21 | Kaur H, Yerra VG, Batchu SN, Tran DT, Kabir MDG, Liu Y, Advani SL, Sedrak P, Geldenhuys L, Tennankore KK, Poyah P, Siddiqi FS, Advani A | 2023 | British Journcal of Pharmacology | Fibrosis | Area Quantification | HALO |
| Exploration of spatial heterogeneity of tumor microenvironment in nasopharyngeal carcinoma via transcriptional digital spatial profiling | Wang L, Wang D, Zeng X, Zhang Q, Wu H, Liu J, Wang Y, Liu G, Poan Y | 2023 | International Journal of Biological Sciences | Oncology | Area Quantification, ISH-IHC/FISH-IF | HALO |
| The role of human endometrial stem cells application in endometrial-factor induced infertility | Bausyte R, Vaigauskaite B, Borutinskaite V, Valatkaite E, Besusparis J, Valkiuniene R, Kazenaite E, Ramasauskaite D, Navakauskiene R | 2023 | Research Square | Other | Area Quantification | HALO |
| Microglial depletion does not impact alphasynuclein aggregation or nigrostriatal degeneration in the rat preformed fibril model | Stoll A, Kemp C, Patterson J, Kubik M, Kuhn N, Benskey M, Duffy M, Luk K, Sortwell C | 2023 | Research Square | Neuroscience | Area Quantification | HALO |
| Therapeutic effects of axitinib, an anti-angiogenic tyrosine kinase inhibitor, on interstitial cystitis | Shin J, Ryu C, Yu H, Park Y, Shin D, Choo M | 2023 | Scientific Reports | Other | Area Quantification | HALO |
| Tumor-infiltrating leukocyte profiling defines three immune subtypes of NSCLC with distinct signaling pathways and genetic alterations | Aoki 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 A | 2023 | Cancer Research Communications | Immuno-oncology | Area Quantification, Cytonuclear | HALO |
| SRF617 Is a Potent Inhibitor of CD39 with Immunomodulatory and Antitumor Properties | Warren M, Matissek S, Rausch M, Panduro M, Hall R, Dulak A, Brennan D, Das Yekkirala S, Koseoglu S, Masia R, Yang Y, Reddy N, Prenovitz R, Strand J, Zaidi T, Devereaux E, Jacoberger Foissac C, Stagg J, Lee B, Holland P, Palombella V, Lake A | 2023 | ImmunoHorizons | Immuno-oncology | Classifier, Area Quantification, Multiplex IHC | HALO |
| Beta-containing bivalent SARS-CoV-2 protein vaccine elicits durable broad neutralization in macaques and protection in hamsters | Berry 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 V | 2023 | Communications Medicine | Infectious Disease | Area Quantification | HALO |
| Context-dependent activation of STING-interferon signaling by CD11b agonists enhances anti-tumor immunity | Liu 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 D | 2023 | Cancer Cell | Immuno-oncology | Area Quantification, Cytonuclear | HALO |
| Reciprocal Interaction of Cancer Stem Cells of Cholangiocarcinoma with Macrophage | Wang X, Golino J, Hawk N, Xie C | 2023 | Stem Cell Reviews and Reports | Oncology | Area Quantification | HALO |
| Mucin 4 is a cellular biomarker of necrotizing bronchiolitis in influenza A virus infection | Arruda B, Kanefsky R, Hau S, Janzen G, Anderson T, Baker A | 2023 | Microbes and Infection | Infectious Disease | Area Quantification | HALO |
| PI3K inhibition circumvents resistance to SHP2 blockade in metastatic triple-negative breast cancer | Amante 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 M | 2023 | Journal of Mammary Gland Biology and Neoplasia | Oncology | Area Quantification | HALO |
| CNS-dominant human FMRP isoform rescues seizures, fear, and sleep abnormalities in Fmr1-KO mice | Wong H, Hooper A, Kang H, Lee S, Zhao J, Sadhu C, Rawat S, Gray S, Hampson D | 2023 | JCI Insight | Neuroscience | Area Quantification | HALO |
| Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesis | Pellegrinelli V, Figueroa-Juárez E, Samuelson I, U-Din M, Rodriguez-Fdez S, Virtue S, Leggat J, Çubuk C, Peirce V, Niemi T, Campbell M, Rodriguez-Cuenca S, Dopazo Blázquez J, Carobbio S, Virtanen K, Vidal-Puig A | 2023 | Cell Reports | Metabolism | Classifier, Area Quantification, Vacuole | HALO |
| Orthotopic model of pancreatic cancer using CD34+ humanized mice and generation of tumor organoids from humanized tumors | Jeong J, Park S, Lee S, Kim Y, Shim I, Jeong S, Choi E, Kim J, Jun E | 2023 | International Immunopharmacology | Immuno-oncology | Area Quantification | HALO |
| The Effects of Acute Ethanol Intoxication on Spinal Cord Injury Outcomes in Female Mice | Glaser E, Stewart A, Jagielo-Miller J, Bailey C, Prendergast M, Gensel J | 2023 | Journal of Neurotrauma | Neuroscience | Area Quantification | HALO |
| Modifying antibody-FcRn interactions to increase the transport of antibodies through the blood-brain barrier | Tien J, Leonoudakis D, Petrova R, Trinh V, Taura T, Sengupta D, Jo L, Sho A, Yun Y, Doan E, Jamin A, Hallak H, Wilson D, Stratton J | 2023 | mABS | Neuroscience | Classifier, Area Quantification, Object Colocalization | HALO |
| The antiviral effects of a MEK1/2 inhibitor promote tumor regression in a preclinical model of human papillomavirus infection-induced tumorigenesis | Luna A, Young J, Sterk R, Bondu V, Schultz F, Kusewitt D, Kang H, Ozbun M | 2023 | Antiviral Research | Oncology, Infectious Disease | Classifier, Area Quantification, Cytonuclear | HALO |
| The Defenders of the Alveolus Succumb in COVID-19 Pneumonia to SARS-CoV-2 and Necroptosis, Pyroptosis and Panoptosis | Schifanella L, Anderson J, Wieking G, Southern P, Antinori S, Galli M, Corbellino M, Lai A, Klatt N, Schacker T, Haase A | 2023 | The Journal of Infectious Disease | Infectious Disease | Area Quantification | HALO |
| Histological validation of atrial structural remodelling in patients with atrial fibrillation | Takahashi 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 K | 2023 | European Heart Journal | Other | Area Quantification | HALO |
| Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling | Reuter 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 RR | 2023 | Communications Biology | Other | Area Quantification | HALO |
| Electrical impedance myography detects dystrophin-related muscle changes in mdx mice | Hiyoshi T, Zhao F, Baba R, Hirakawa T, Kuboki R, Suzuki K, Tomimatsu Y, O'Donnell P, Han S, Zach N, Nakashima M | 2023 | Research Square | Myology | Area Quantification, Muscle Fiber | HALO |
| Altered expression, but small contribution, of the histone demethylase KDM6A in obstructive uropathy in mice | Hong LYQ, Yeung ESH, Tran DT, Yerra VGY, Kaur HK, Kabir MDG, Advani SL, Liu Y, Batchu SN, Advani A | 2023 | Disease Models & Mechanisms | Gastroenterology | Area Quantification, Object Colocalization | HALO |
| Amyloid-β (Aβ) immunotherapy induced microhemorrhages are associated with activated perivascular macrophages and peripheral monocyte recruitment in Alzheimer’s disease mice | Taylor X, Clark I, Fitzgerald G, Oluoch H, Hole J, DeMattos R, Wang Y, Pan F | 2023 | Molecular Neurodegeneration | Immuno-oncology, Neuroscience | Area Quantification | HALO |
| Desialylated platelet clearance in the liver is a novel mechanism of systemic immunosuppression | Li J, Karakas D, Xue F, Chen Y, Zhu G, Ycel Y, MacParland S, Zhang H, Semple J, Freedman J, Shi Q, Ni H | 2023 | Research | Immunology | Area Quantification | HALO |
| SMRT Sequencing Enables High-Throughput Identification of Novel AAVs from Capsid Shuffling and Directed Evolution | Widler Casy, Garza IT, Chen X, Dong T, Hu Y, Kanchwala M, Trygg CB, Shyng C, Xing C, Bunnell BA, Braun SE, Gray SJ | 2023 | Genes | Other | Area Quantification | HALO |
| Differential effects of PGAM5 knockout on high fat high fructose diet and methionine choline-deficient diet induced non-alcoholic steatohepatitis (NASH) in mice | Li L, Guo C, Yu Y, Tie L, Lu G, Liu F, Han X, Ji L, Zou X | 2023 | Cell & Bioscience | Metabolism | Area Quantification, Multiplex IHC | HALO |
| Rosmarinic acid alleviates intestinal inflammatory damage and inhibits endoplasmic reticulum stress and smooth muscle contraction abnormalities in intestinal tissues by regulating gut microbiota | Li K, Wu J, Xu S, Li X, Zhang Y, Gao X | 2023 | Microbiology Spectrum | Infectious Disease | Area Quantification | HALO |
| Investigating the Effects of Stereotactic Body Radiation Therapy on Pancreatic Tumor Hypoxia and Microvasculature in an Orthotopic Mouse Model using Intravital Fluorescence Microscopy | Samuel T, Rapic S, Lindsay P, DaCosta RS | 2023 | Research Square | Oncology | Classifier, Area Quantification | HALO |
| Regional and cellular iron deposition patterns predict clinical subtypes of multiple system atrophy | Lee S, Martinez-Valbuena I, Lang AE, Kovacs GG | 2023 | Research Square | Neuroscience | Area Quantification, Object Colocalization | HALO |
| A novel retinoic acid receptor-γ agonist antagonizes immune checkpoint resistance in lung cancers by altering the tumor immune microenvironment | Wei 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 X | 2023 | Scientific Reports | Immuno-oncology | Area Quantification, Cytonuclear | HALO, HALO AI |
| Gys1 Antisense Therapy Prevents Disease-Driving Aggregates and Epileptiform Discharges in a Lafora Disease Mouse Model | Donohue 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 M | 2023 | Neurotherapeutics | Neuroscience | Area Quantification | HALO |
| Parvalbumin in the metabolic pathway of glutamate and γ-aminobutyric acid: Influence on expression of GAD65 and GAD67 | Zeng C, Lei D, Lu Y, Huang Q, Wu Y, Yang S, Wu Y | 2023 | Archives of Biochemistry and Biophysics | Neuroscience | Area Quantification | HALO |
| A phase I, first-in-human study of TAK-164, an antibody–drug conjugate, in patients with advanced gastrointestinal cancers expressing guanylyl cyclase C | Kim R, Leal A, Parikh A, Ryan D, Wang S, Bahamon B, Gupta N, Moss A, Pye J, Miao H, Inguilizian H, Cleary J | 2023 | Cancer Chemotherapy and Pharmacology | Oncology | Area Quantification | HALO |
| Novel read through agent: ZKN-0013 demonstrates efficacy in APCmin model of familial adenomatous polyposis | Graf M, Apte S, Terzo E, Padhye S, Shi S, Cox M, Clark R, Modur V, Badarinarayana V | 2023 | Journal of Molecular Medicine | Oncology | Area Quantification | HALO |
| p38MAPKa stromal reprogramming sensitizes metastatic breast cancer to immunotherapy | Faget 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 S | 2023 | Cancer Discovery | Immuno-oncology | Area Quantification | HALO |
| Vascular-Parenchymal Crosstalk Promotes Lung Fibrosis Through BMPR2 Signaling | Yanagihara 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 M | 2023 | American Journal of Respiratory and Critical Care Medicine | Fibrosis | Area Quantification, ISH, TMA | HALO |
| T cell immunotherapies engage neutrophils to eliminate tumor antigen escape variants | Hirschhorn 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 T | 2023 | Cell | Area Quantification, Highplex FL | HALO | |
| 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 study | Li S, Zhang M, Wang B, Li X, Liang G | 2023 | Xenobiotica | Gastroenterology | Area Quantification | HALO |
| Phase I Study of SYNB1891, an Engineered E. coli Nissle Strain Expressing STING Agonist, with and without Atezolizumab in Advanced Malignancies | Luke J, Piha-Paul S, Medina T, Verschraegen C, Varterasian M, Brennan A, Rise R, Sokolovska A, Strauss J, Hava D, Janku F | 2023 | Clinical Cancer Research | Immuno-oncology | Area Quantification | |
| Hepatic proinflammatory myeloid phenotypes are a hallmark of Ebola virus Kikwit pathogenesis in rhesus monkeys | Tseng A, Carossino M, Gertje H, O'Connell A, Gummuluru S, Kolachalama V, Balasuriya U, Connor J, Bennett R, Liu D, Hensley L, Crossland N | 2023 | Veterinary Pathology | Infectious Disease | Area Quantification, Highplex FL | HALO |
| Nicotinamide N-methyltransferase sustains a core epigenetic program that promotes metastatic colonization in breast cancer | Pinto 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 M | 2023 | The EMBO Journal | Oncology | Area Quantification, Multiplex IHC | HALO, HALO AI |
| Effect of Dupilumab on Type 2 Biomarkers in Chronic Rhinosinusitis With Nasal Polyps: SINUS-52 Study Results | Bachert 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 L | 2023 | Annals of Otology, Rhinology & Laryngology | Other | Area Quantification | HALO, HALO AI |
| Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression | Macke A, Pachikov A, Divita T, Morris M, LaGrange C, Holzapfel M, Kubyshkin A, Zyablitskaya E, Makalish T, Eremenko S, Qiu H, Riethoven J, Hemstreet G, Petrosyan A | 2023 | Molecular Cancer Research | Oncology | Classifier, Area Quantification, Multiplex IHC, TMA | HALO |
| ASK1 inhibitors are potential pan-antiviral drugs, which dampen replication of diverse viruses including SARS-CoV2 | Demian W, Jacob R, Cormier O, Nazli A, Melki M, Asavajaru A, Baid K, Zhang A, Miller M, Kaushic C, Banerjee A, Mossman K | 2023 | Antiviral Research | Infectious Disease | Area Quantification | HALO |
| Empowering Renal Cancer Management with AI and Digital Pathology: Pathology, Diagnostics and Prognosis | Ivanova E, Fayzullin A, Grinin V, Ermilov D, Arutyunyan A, Timashev P, Shekhter A | 2023 | Biomedicines | Review | Classifier, Area Quantification, Object Colocalization | HALO, HALO AI |
| Unaltered hepatic wound healing response in male rats with ancestral liver injury | Beil J, Perner J, Pfaller L, Gérard M, Piaia A, Doelemeyer A, Wasserkrug Naor A, Martin L, Piequet A, Dubost V, Chibout S, Moggs J, Terranova R | 2023 | Nature Communications | Other | Classifier, Area Quantification | HALO, HALO AI |
| Disease pathology signatures in a mouse model of Mucopolysaccharidosis type IIIB | Petrova R, Patil AR, Trinh V, McElroy KE, Bhakta M, Tien J, Wilson DS, Warren L, Stratton JR | 2023 | Scientific Reports | Neuroscience, Metabolism | Classifier, Area Quantification, Object Colocalization | HALO |
| Seeding the aggregation of TDP-43 requires post-fibrillization proteolytic cleavage | Kumar ST, Nazarov S, Porta S, Majarjan N, Cendrowska U, Kabani M, Finamore F, Xu Y, Lee VMY, Lashuel HA | 2023 | Nature Neuroscience | Neuroscience | Area Quantification, Highplex FL | HALO |
| Donor IL-17 receptor A regulates LPS-potentiated acute and chronic murine lung allograft rejection | Watanabe T, Juvet SC, Berra G, Havlin J, Zhong W, Boonstra K, Daigneault T, Horie M, Konoeda C, Teskey G, Guan Z, Hwang DM, Liu M, Keshavjee S, Martinu T | 2023 | JCI Insight | Immunology, Fibrosis | Area Quantification | HALO |
| A2ML1 Inhibits Esophageal Squamous Cell Carcinoma Progression and Serves as a Novel Prognostic Biomarker | Zhang X, Tang C, Lian J, Jiang Y | 2023 | Canadian Journal of Gastroenterology and Hepatology | Oncology | Area Quantification | 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 apelin‑apelin receptor signaling pathway in fibroblasts is involved in tumor growth via p53 expression of cancer cells | Saiki H, Hayashi Y, Yoshii S, Kimura E, Nakagawa K, Kato M, Uema R, Inoue T, Sakatani A, Yoshihara T, Tsujii Y, Shinzaki S, Iijima H, Takehara T | 2023 | International Journal of Oncology | Oncology | Area Quantification | HALO |
| Parishin treatment alleviates cardiac aging in naturally aged mice | Zhou S, Zhao X, Wu L, Yan R, Sun L, Zhang Q, Gong C, Liu Y, Xiang L, Li S, Wang P, Yang Y, Ren W, Jiang J, Yang Y | 2023 | Heliyon | Other | Area Quantification, Multiplex IHC | HALO |
| Fecal microbiota transplanted from old mice promotes more colonic inflammation, proliferation, and tumor formation in azoxymethane-treated A/J mice than microbiota originating from young mice | Crossland NA, Beck S, Tan WY, Lo M, Mason JB, Zhang C, Guo W, Crott JW | 2023 | Gut Microbes | Other | Area Quantification, Highplex FL | HALO |
| Intratracheally Administered Peptide-Modified Lipid Admixture Containing Fasudil and/or DETA NONOate Ameliorates Various Pathologies of Pulmonary Arterial Hypertension | Sarkar T, Moinuddin SM, Isbatan A, Chen J, Mann D, Ahsan F | 2023 | Pharmaceuticals | Other | Area Quantification | HALO |
| Chiral metal-organic frameworks incorporating nanozymes as neuroinflammation inhibitors for managing Parkinson’s disease | Jiang W, Li Q, Zhang R, Li J, Lin Q, Li J, Zhou X, Yan X, Fan K | 2023 | Nature Communications | Neuroscience | Area Quantification | HALO |
| COVID-19 and influenza infections mediate distinct pulmonary cellular and transcriptomic changes | Wang C, Khatun M S, Zhang Z, Allen M J, Chen Z, Ellsworth C R, Currey J M, Dai G, Tian D, Bach K, Yin X-M, Traina-Dorge V, Rappaport J, Maness N J, Blair R V, Kolls J K, Pociask D A, Qin X | 2023 | Communications Biology | Infectious Disease | Area Quantification, Highplex FL, Figure Maker | HALO, HALO AI |
| ApoER2-Dab1 disruption as the origin of pTau-associated neurodegeneration in sporadic Alzheimer’s disease | Ramsden C, Zamora D, Horowitz M, Jahanipour J, Calzada E, Li X, Keyes G, Murray H, Curtis M, Faull R, Sedlock A, Maric D | 2023 | Acta Neuropathologica Communications | Neuroscience | Area Quantification, Object Colocalization | HALO |
| Mesenchymal cells support the early retention of primary alveolar type 2 cells on acellular mouse lung scaffolds | Taniguchi D, Ahmadipour M, Eiliazadeh A, Duchesneau P, Nagayasu T, Haykal S, Karoubi G, Waddell T | 2023 | Regenerative Therapy | Other | Area Quantification | HALO |
| RFX6 facilitates aerobic glycolysis‐mediated growth and metastasis of hepatocellular carcinoma through targeting PGAM1 | Qiu Z, Wang C, Huang P, Yuan Y, Shi Y, Lin Z, Huang Z, Zuo D, Qiu J, He W, Shen J, Niu Y, Yuan Y, Li B | 2023 | Clinical and Translational Medicine | Oncology | Area Quantification, Multiplex IHC | HALO |
| Complex Urban Atmospheres alters Alveolar Stem Cells Niche Properties and drives Lung Fibrosis | Belgacemi R, Baptista BR, Justeau G, Toigo M, Frauenpreis A, Yilmaz R, Der Vartanian A, Cazaunau M, Pangui E, Bergé A, Gratien A, Macias Rodriguez JC, Bellusci S, Derumeaux G, Boczkowski J, Al Alam D, Coll P, Lanone S, Boyer L | 2023 | American Journal of Physiology - Lung Cellular and Molecular Physiology | Fibrosis | Classifier, Area Quantification, Highplex FL | HALO |
| Antimicrobial activity of yak beta-defensin 116 against Staphylococcus aureus and its role in gut homeostasis | Li B, Zhang L, Wang L, Wei Y, Guan J, Mei Q, Hao N | 2023 | International Journal of Biological Macromolecules | Infectious Disease | Area Quantification | HALO |
| A microtubule stabilizer ameliorates protein pathogenesis and neurodegeneration in mouse models of repetitive traumatic brain injury | Zhao X, Zeng W, Xu H, Sun Z, Hu Y, Peng B, McBride JD, Duan J, Deng J, Zhang B, Kim SJ, Zoll B, Saito T, Sasaguri H, Saido TC, Ballatore C, Yao H, Wang Z, Trojanowski JQ, Brunden KR, Lee VMY, He Z | 2023 | Science Translational Medicine | neuroscience | Area Quantification, Object Colocalization, Multiplex IHC | HALO |
| A novel porous hydroxyapatite scaffold (pHAMG) enhances angiogenesis and osteogenesis around dental implants by regulating the immune microenvironment | Li P, Zhou X, Xun Q, Zheng J, Mu Y, Liao J | 2023 | Clinical Oral Investigations | Other | Area Quantification | HALO |
| An antibody-drug conjugate directed to tissue factor shows preclinical anti-tumor activity in head and neck cancer as a single agent and in combination with chemoradiotherapy | Bakema J E, Stigter-van Walsum M, Harris J R, Ganzevles S H, Muthuswamy A, Houtkamp M, Plantinga T S, Bloemena E, Brakenhoff R H, Breij E C W, van de Ven R | 2023 | Molecular Cancer Therapeutics | Oncology | Area Quantification | HALO |
| Amelioration of Tumor-Promoting Microenvironment via Vascular Remodeling and CAF Suppression using E7130: Biomarker Analysis by Multi-modal Imaging Modalities | Ito K, Yamaguchi M, Semba T, Tabata K, Tamura M, Aoyama M, Abe T, Asano O, Terada Y, Funashashi Y, Fujii H | 2023 | Molecular Cancer Therapeutics | Oncology | Area Quantification, Object Colocalization | HALO |
| Impact of tectoridin on the pharmacokinetics of florfenicol via targeting cytochrome P450 and P-glycoprotein of rats | Zhang M, Wang B, Li X, Yin Q, Liang G, Li S | 2023 | Xenobiotica | Other | Area Quantification | HALO |
| Inulin-like polysaccharide ABWW may impede CCl4 induced hepatic stellate cell activation through mediating the FAK/PI3K/AKT signaling pathway in vitro & in vivo | Dai X, Du Z, Jin C, Tang B, Chen X, Jing X, Shen Y, He F, Wang S, Li J, Ding K, Zang Y | 2023 | Carbohydrate Polymers | Fibrosis | Area Quantification | HALO |
| A modified mouse model of Friedreich's ataxia with conditional Fxn allele homozygosity delays onset of cardiomyopathy | Perfitt TL, Huichalaf C, Gooch R, Kuperman A, Ahn Y, Chen X, Ullas S, Hirenallur-Shanthappa D, Zhan Y, Otis D, Whiteley LO, Bulawa C, Martelli A | 2023 | American Journal of Physiology-Heart and Circulatory Physiology | Other | Classifier, Area Quantification | HALO |
| Electroacupuncture at Sensitized Acupoints Relieves Somatic Referred Pain in Colitis Rats by Inhibiting Sympathetic-Sensory Coupling to Interfere with 5-HT Signaling Pathway | Yang Y, Qu J, Guo H, Zhou H, Ruan X, Peng Y, Shen X, Xiong J, Wang Y. | 2023 | Chinese Journal of Integrative Medicine | Gastroenterology | Area Quantification | HALO |
| Enterococcus faecium inhibits NF-κB / NLRP3 / Caspase-1 signaling pathway to antagonize enterotoxigenic Escherichia coli-mediated inflammatory response | Zheng H, Pu S, Liu J, Yang F, Chen D | 2023 | Canadian Journal of Microbiology | Infectious Disease | Area Quantification | HALO |
| ERBB3 overexpression is enriched in diverse patient populations with castration-sensitive prostate cancer and is associated with a unique AR activity signature | Vellky J E, Kirkpatrick B J, Gutgesell L C, Morales M, Brown R M, Wu Y, Maienschein-Cline M, Notardonato L D, Weinfeld M S, Nguyen R H, Brister E, Sverdlov M, Liu L, Xu Z, Kregel S, Nonn L, Vander Griend D J, Reizine N M | 2024 | Clinical Cancer Research | Oncology | Area Quantification, TMA | HALO, HALO AI |
| Multiplex analysis of intratumoural immune infiltrate and prognosis in patients with stage II–III colorectal cancer from the SCOT and QUASAR 2 trials: a retrospective analysis | Frei AL, McGuigan A, Sinha RAK, Jabbar F, Gneo L, Tomasevic T, Harkin A, Iveson T, Saunders MP, Oien KA, Maka N, Pezzella F, Campo L, Browne M, Glaire M, Kildal W, Danielsen HE, Hay J, Edwards J, Sansom O, Kelly C, Tomlinson I, Kerr R, Kerr D, Domingo E, consortium T, Church DN, Koelzer VH | 2024 | The Lancet Oncology | Immuno-oncology | Area Quantification, Highplex FL, TMA | HALO, HALO AI |
| Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer | Malla S B, Byrne R M, Lafarge M W, Corry S M, Fisher N C, Tsantoulis P K, Mills M L, Ridgway R A, Lannagan T R M, Najumudeen A K, Gilroy K L, Amirkhah R, Maguire S L, Mulholland E J, Belnoue-Davis H L, Grassi E, Viviani M, Rogan E, Redmond K L, Sakhnevych S, McCooey A J, Bull C, Hoey E, Sinevici N, Hall H, Ahmaderaghi B, Domingo E, Blake A, Richman S D, Isella C, Miller C, Bertotti A, Trusolino L, Loughrey M B, Kerr E M, Tejpar S, Maughan T S, Lawler M, Campbell A D, Leedham S J, Koelzer V H, Sansom O J, Dunne P D | 2024 | Nature Genetics | Oncology | Area Quantification | HALO |
| Homocysteine potentiates amyloid 훃-induced death receptor 4- and 5-mediated cerebral endothelial cell apoptosis, blood brain barrier dysfunction and angiogenic impairment | Carey A, Parodi-Rullan R, Vazquez-Torres R, Canepa E, Fossati S | 2024 | Aging Cell | Neuroscience | Area Quantification | HALO |
| Identification of tyrosine brominated extracellular matrix proteins in normal and fibrotic lung tissues | Cruz LC, Habibovic A, Dempsey B, Massafera MP, Janssen-Heininger YM, Lin MJ, Hoffman ET, Weiss DJ, Huang SK, van der Vliet A, Meotti FC | 2024 | Redox Biology | Fibrosis | Area Quantification, Highplex FL | HALO |
| BCL-XL inhibitors enhance the apoptotic efficacy of BRAF inhibitors in BRAFV600E colorectal cancer | Jenkins L, Luk I, Chionh F, Tan T, Needham K, Ayton J, Reehorst C, Vukelic N, Sieber O, Mouradov D, Gibbs P, Williams D, Tebbutt N, Desai J, Hollande F, Dhillon A, Lee E, Merino D, Fairlie W, Mariadason J | 2024 | Cell Death & Disease | Oncology | Area Quantification | HALO |
| Carrier-Free, Amorphous Verteporfin Nanodrug for Enhanced Photodynamic Cancer Therapy and Brain Drug Delivery | Quinlan J A, Inglut C T, Srivastava P, Rahman I, Stabile J, Gaitan B, Valle C A D, Baumiller K, Gaur A, Chiou W A, Karim B, Connolly N, Robey R W, Woodworth G F, Gottesman M M, Huang H C H | 2024 | Advanced Science | Oncology | Area Quantification | HALO |
| A small-molecule TNIK inhibitor targets fibrosis in preclinical and clinical models | Ren F, Aliper A, Chen J, Zhao H, Rao S, Kuppe C, Ozerov I V, Zhang M, Witte K, Kruse C, Aladinskiy V, Ivanenkov Y, Polykovskiy D, Fu Y, Babin E, Qiao J, Liang X, Mou Z, Wang H, Pun F W, Ayuso P T, Veviorskiy A, Song D, Liu S, Zhang B, Naumov V, Ding X, Kukharenko A, Izumchenko E, Zhavoronkov A | 2024 | Nature Biotechnology | Fibrosis | Area Quantification | HALO |
| Delivery of a BET protein degrader via a CEACAM6-targeted antibody–drug conjugate inhibits tumour growth in pancreatic cancer models | Nakazawa Y, Miyano M, Tsukamoto S, Kogai H, Yamamoto A, Iso K, Inoue S, Yamane Y, Yabe Y, Umihara H, Taguchi J, Akagi T, Yamaguchi A, Koga M, Toshimitsu K, Hirayama T, Mukai Y, Machinaga A | 2024 | Nature Communications | Oncology | Area Quantification | HALO |
| MSUT2 regulates tau spreading via adenosinergic signaling mediated ASAP1 pathway in neurons | Xu H, Qiu Q, Hu P, Hoxha K, Jang E, O'Reilly M, Kim C, He Z, Marotta N, Changolkar L, Zhang B, Wu H, Schellenberg G D, Kraemer B, Luk K C, Lee E B, Trojanowski J Q, Brunden K R, Lee V M-Y | 2024 | Acta Neuropathologica | Neuroscience | Area Quantification | HALO |
| A single nuclear transcriptomic characterisation of mechanisms responsible for impaired angiogenesis and blood-brain barrier function in Alzheimer’s disease | Tsartsalis S, Sleven H, Fancy N, Wessely F, Smith A M, Willumsen N, Cheung T K D, Rokicki M J, Chau V, Ifie E, Khozoie C, Ansorge O, Yang X, Jenkyns M H, Davey K, McGarry A, Muirhead R C J, Debette S, Jackson J S, Montagne A, Owen D R, Miners J S, Love S, Webber C, Cader M Z, Matthews P M | 2024 | Nature Communications | Neuroscience | Area Quantification, Multiplex IHC | HALO |
| Translational and Therapeutic Evaluation of RAS-GTP Inhibition by RMC-6236 in RAS-Driven Cancers | Jiang J, Jiang L, Maldonato B J, Wang Y, Holderfield M, Aronchik I, Winters I P, Salman Z, Blaj C, Menard M, Brodbeck J, Chen Z, Wei X, Rosen M J, Gindin Y, Lee B J, Evans J W, Chang S, Wang Z, Seamon K J, Parsons D, Cregg J, Marquez A, Tomlinson A C A, Yano J K, Knox J E, Quintana E, Aguirre A J, Arbour K C, Reed A, Gustafson W C, Gill A L, Koltun E S, Wildes D, Smith J A M, Wang Z, Singh M | 2024 | Cancer Discovery | Oncology | Classifier, Area Quantification, Cytonuclear | HALO |
| Direct and selective pharmacological disruption of the YAP–TEAD interface by IAG933 inhibits Hippo-dependent and RAS–MAPK-altered cancers | Chapeau E, Sansregret L, Galli G, Chène P, Wartmann M, Mourikis T, Jaaks P, Baltschukat S, Barbosa I, Bauer D, Brachmann S, Delaunay C, Estadieu C, Faris J, Furet P, Harlfinger S, Hueber A, Núñez E, Kodack D, Mandon E, Martin T, Mesrouze Y, Romanet V, Scheufler C, Schmelzle T | 2024 | Nature Cancer | Oncology | Area Quantification, Cytonuclear | HALO |
| Landscape of brain myeloid cell transcriptome along the spatiotemporal progression of Alzheimer’s disease reveals distinct sequential responses to Aβ and tau | Wachter A, Woodbury M E, Lombardo S, Abdourahman A, Wuest C, McGlame E, Pastika T, Tamm J, Romanul N, Yanamandra K, Bennett R, Lin G, Kwon T, Liao F, Klein C, Grinberg Y, Jaisa-aad M, Li H, Frosch M P, Kummer M P, Das S, Dellovade T, Karran E H, Langlois X, Ried J S, Serrano-Pozo A, Talanian R V, Biber K, Hyman B T | 2024 | Acta Neuropathologica | Neuroscience | Area Quantification | HALO |
| Conserved immuno-collagenic subtypes predict response to immune checkpoint blockade | Mei J, Cai Y, Xu R, Li Q, Chu J, Luo Z, Sun Y, Shi Y, Xu J, Li D, Li S, Jiang Y, Liu J, Qian Z, Zhou J, Wan M, Yang Y, Zhu Y, Zhang Y, Yin Y | 2024 | Cancer Communications | Immuno-oncology | Area Quantification | HALO |
| N6-methyladenosine-modified circSLCO1B3 promotes intrahepatic cholangiocarcinoma progression via regulating HOXC8 and PD-L1 | Li J, Xu X, Xu K, Zhou X, Wu K, Yao Y, Liu Z, Chen C, Wang L, Sun Z, Jiao D, Han X | 2024 | Journal of Experimental & Clinical Cancer Research | Oncology | Area Quantification, FISH, Highplex, TMA | HALO |
| Presynaptic density determined by SV2A PET is closely associated with postsynaptic metabotropic glutamate receptor 5 availability and independent of amyloid pathology in early cognitive impairment | Wang J, Huang Q, He K, Li J, Guo T, Yang Y, Lin Z, Li S, Vanderlinden G, Huang Y, Laere K, Guan Y, Guo Q, Ni R, Li B, Xie F | 2024 | Alzheimer's & Dementia | Neuroscience | Area Quantification | HALO |
| Alpha-synuclein inclusion responsive microglia are resistant to CSF1R inhibition | Stoll AC, Kemp CJ, Patterson JR, Kubik M, Kuhn N, Benskey M, Duffy MF, Luk KC, Sortwell CE | 2024 | Journal of Neuroinflammation | Neuroscience | Area Quantification | HALO |
| A small-molecule microtubule-stabilizing agent safely reduces Aβ plaque and tau pathology in transgenic mouse models of Alzheimer’s disease | Yao Y, Muench M, Alle T, Zhang B, Lucero B, Perez-Tremble R, McGrosso D, Newman M, Gonzalez DJ, Lee VMY, Ballatore C, Brunden KR | 2024 | Alzheimer's & Dementia | Neuroscience | Area Quantification | HALO |
| Inhibition of mRNA nuclear export promotes SARS-CoV-2 pathogenesis | Mei M, Cupic A, Miorin L, Ye C, Cagatay T, Zhang K, Patel K, Wilson N, McDonald W, Crossland N, Lo M, Rutkowska M, Aslam S, Mena I, Martinez-Sobrido L, Ren Y, García-Sastre A, Fontoura B | 2024 | Proceedings of the National Academy of Sciences | Infectious Disease | Area Quantification | HALO |
| Spatial distribution of Mycobacterium tuberculosis mRNA and secreted antigens in acid-fast negative human antemortem and resected tissue | Nargan K, Glasgow J, Nadeem S, Naidoo T, Wells G, Hunter R, Hutton A, Lumamba K, Msimang M, Benson P, Steyn A | 2024 | EBioMedicine | Infectious Disease | Area Quantification, ISH | HALO |
| Unsupervised Segmentation of 3D Microvascular Photoacoustic Images Using Deep Generative Learning | Sweeney PW, Hacker L, Lefebvre TL, Brown L, Gröhl J, Bohndeik SE | 2024 | Advanced Science | Other | Area Quantification | HALO |
| The miR-29 family facilitates the activation of NK-cell immune responses by targeting the B7-H3 immune checkpoint in neuroblastoma | Pathania AS, Chava H, Chaturvedi NK, Chava S, Byrareddy SN, Coulter DW, Challagundla KB | 2024 | Cell Death & Disease | Immuno-oncology | Area Quantification | HALO |
| Combined inhibition of KRASG12C and mTORC1 kinase is synergistic in non-small cell lung cancer | Kitai H, Choi P H, Yang Y C, Boyer J A, Whaley A, Pancholi P, Thant C, Reiter J, Chen K, Markov V, Taniguchi H, Yamaguchi R, Ebi H, Evans J, Jiang J J, Lee B, Wildes D, Stanchina E, Smith J A M, Singh M, Rosen N | 2024 | Nature Communications | Oncology | Classifier, Area Quantification, Mulitplex iHC | HALO |
| Phosphodiesterase-5 inhibition collaborates with vaccine-based immunotherapy to reprogram myeloid cells in pancreatic ductal adenocarcinoma | Gross N, Zhang Z, Mitchell J T, Charmsaz S, Hernandez A G, Coyne E M, Shin S M, Vargas Carvajal D C, Sidiropoulos D N, Cho Y, Mo G, Yuan X, Cannon C, Suresh Babu J, Lyman M R, Armstrong T, Kagohara L T, Bever K M, Le D T, Jaffee E M, Fertig E J, Ho W J | 2024 | JCI Insight | Immuno-oncology | Area Quantification | HALO |
| Metabolic imaging across scales reveals distinct prostate cancer phenotypes | Sushentsev N, Hamm G, Flint L, Birtles D, Zakirov A, Richings J, Ling S, Tan J Y, McLean M A, Ayyappan V, Menih I H, Brodie C, Miller J L, Mills I G, Gnanapragasam V J, Warren A Y, Barry S T, Goodwin R J A, Barrett T, Gallagher F A | 2024 | Nature Communications | Oncology | Area Quantification, FISH, Membrane, Multiplex IHC | HALO, HALO AI |
Related HALO Modules
Quantify expression of up to five brightfield stains in any cellular compartment - membrane, nucleus or cytoplasm.
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Quantify expression of an unlimited number of biomarkers in any cellular compartment - membrane, nucleus or cytoplasm.
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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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