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HALO® Module

Area Quantification FL

Area Quantification FL is a flexible area-based analysis module for quantifying an unlimited number of fluorescent dyes.  It is a flexible alternative for analyzing images where cell structure cannot be readily identified or where tissue area-based outputs are more reliable or meaningful measure.  Area Quantification FL quantifies and reports dye positive area, average intensity for each dye, binned positivity based on intensity (0, 1+, 2+ and 3+) and area of colocalization (when multiple dyes are analyzed).

Note that the Indica Labs’ Area Quantification FL 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!

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

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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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Highplex FL

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

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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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