Indica
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Area Quantification FL

intensity markup single dye intensity markup single dye colocalization markup colocalization markup

Area Quantification FL

 

Product Overview

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).

In the first example shown above, the dye positive area for the green dye is shown with the intensity overlay such that weak positive pixels (1+) show as yellow in the markup, moderate positive pixels (2+) are orange and strong positive pixels (3+) are red.  In the second example image, the colocalization markup shows areas positive for green dye in green, red dye in red, and areas of colocalization in yellow.

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

The Area Quantification FL module integrates seamlessly into the   HALO™ platform which is compatible with a number of third party systems and  file formats.

Contact info@indicalab.com for product demonstration and pricing information or upload some images for a free trial.

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).

In the first example shown above, the dye positive area for the green dye is shown with the intensity overlay such that weak positive pixels (1+) show as yellow in the markup, moderate positive pixels (2+) are orange and strong positive pixels (3+) are red.  In the second example image, the colocalization markup shows areas positive for green dye in green, red dye in red, and areas of colocalization in yellow.

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

HALO is compatible with a broad spectrum of image and digital slide formats.  Yours not on the list? Email us your requirements.

Non-proprietary (JPG, TIF)
Nikon (ND2)
3D Histech (MRXS)
Perkin Elmer (QPTIFF, component TIFF)
Olympus (VSI)
Hamamatsu (NDPI, NDPIS)
Aperio (SVS, AFI)
Zeiss (CZI)
Leica (SCN, LIF)
Philips (Requires Philips IMS)

Here are a few publications that cite use of the Area Quantification Brightfield or FL modules.  Your publication not on the list?  Drop us an email to let us know about it!

 

TitleAuthorsYearJournalApplicationHALO Modules
Anti-NKG2A mAb Is a Checkpoint Inhibitor that Promotes Anti-tumor Immunity by Unleashing Both T and NK CellsAndre ́P, Denis C, Soulas C, Bourbon-Caillet C, Lopez J, Arnoux T, Bléry M, Bonnafous C, Gauthier L, Morel A, Rossi B, Remark R, Breso V, Bonnet E, Habif G, Guia S, Lalanne AI, Hoffmann C, Lantz O, Fayette J, Boyer-Chammard A, Zerbib R, Dodion P, Ghadially H, Jure-Kunkel M, Morel Y, Herbst R, Narni-Mancinelli E, Cohen RB, Vivier E2018CellOncology, Immuno-oncologyArea Quantification, Cytonuclear
The R-enantiomer of ketorolac delays mammary tumor development in mouse mammary tumor virus-polyoma middle T antigen (MMTV-PyMT) mice AS Peretti, D Dominguez, MM Grimes, HJ Hathaway, ER Prossnitz, MR Rivera, A Wandinger-Ness, D Kusewitt, LG Hudson2017The American Journal of PathologyOncologyClassifier, Area Quantification, Cytonuclear
Selective modulation of the androgen receptor AF2 domain rescues degeneration in spinal bulbar muscular atrophy Badders NM, Korff A, Miranda HC, Vuppala PK, Smith RB, Winborn BJ, Quemin ER, Sopher BL, Dearman J, Messing J, Kim NC, Moore J, Freibaum BD, Kanagaraj AP, Fan B, Tillman H, Chen P-C, Wang Y, Freeman BB, Li Y, Kim HJ, La Spada AR, Taylor JP2018Nature MedicineMyologyArea Quantification
Efficacy of injectable praziquantel for elimination of trematode metacercariae in bluegills (Lepomis macrochirus) and quantification of parasite death by propidium iodide staining Bader C, Chelladurai JJ, Starling DE, Jones DE, Brewer MT2017Parasitology ResearchInfectious DiseaseArea Quantification
Both brown adipose tissue and skeletal muscle thermogenesis processes are activated during mild to severe cold adaptation in mice Bal NC, Singh S, Reis FCG, Maurya SK, Pani S, Rowland LA, Periasamy M2017Journal of Biological ChemistryMyologyArea Quantification
Sex- and Dose-Specific Effects of Maternal Bisphenol A Exposure on Pancreatic Islets of First- and Second-Generation Adult Mice Offspring Bansal A, Rashid C, Xin F, Li C, Polyak E, Duemler A, van der Meer T, Stefaniak M, Wajid S, Doliba N, Bartolomei MS, Simmons RA2017Environmental Health PerspectivesMetabolismArea Quantification
Stem cell–derived CAR T cells traffic to HIV reservoirs in macaquesBarber-Axthelm IM, Barber-Axthelm V, Sze KY, Zhen A, Suryawanshi GW, Chen ISY, Zack JA, Kitchen SG, Kiem H-P, Peterson CW2021JCI InsightImmunology, Infectious DiseaseArea Quantification
Cutaneous pharmacologic cAMP induction induces melanization of the skin and improves recovery from ultraviolet injury in melanocortin 1 receptor‐intact or heterozygous skin Bautista R-M, Carter KM, Jarrett SG, Napier D, Wakamatsu K, Ito S, D'Orazio JA2019Pigment Cell & Melanoma ResearchDermatologyArea Quantification
Tuning of delta-protocadherin adhesion through combinatorial Bisogni AJ, Ghazanfar S, Williams EO, Marsh HM, Yang JYH, Lin DM2018eLifeNeuroscienceArea Quantification
Unmasking of oestrogen‐dependent changes in left ventricular structure and function in aged female rats: a potential model for pre‐heart failure with preserved ejection fractionBustamante M, Garate‐Carrillo A, Ito BR, Garcia R, Carson N, Ceballos G, Ramirez‐Sanchez I, Omens J, Villarreal F2019The Journal of PhysiologyMyologyArea Quantification, Laer Thickness
Epithelial-mesenchymal transition of absorptive enterocytes and depletion of Peyer's patch M cells after PEDV infectionChen Y-M, Helm ET, Groeltz-Thrush, Gabler NK, Burrough ER2020VirologyImmunologyArea Quantification
Glucagon contibutes to liver zonation Cheng X, Kim SK, Okamoto H, Xin Y, Yancopoulos GD, Murphy AJ, Gromada J2018Proceedings of the National Academy of SciencesMetabolismArea Quantification
Impact of Preanalytical Factors During Histology Processing on Section Suitability for Digital Image AnalysisChlipala EA, Butters M, Brous M, Fortin JS, Archuletta R, Copeland K, Bolon B2020Toxicologic PathologyToxicologyArea Quantification, Cytonuclear
Methacrylic Acid Copolymer Coating Enhances Constructive Remodeling of Polypropylene Mesh by Increasing the Vascular Response Coindre VF, Carleton MM, Sefton MV2019Advanced Healthcare MaterialsBiomaterialsArea Quantification
Cognitive and Pathological Influences of Tau Pathology in Lewy Body Disorders Coughlin DG, Xie SX, Liang M, Williams A, Peterson C, Weintraub D, McMillan CT, Wolk DA, Akhtar RS, Hurtig H, Coslett HB, Hamilton R, Siderowf A, Duda JE, Rascovsky K, Lee EB, Lee VM-Y, Grossman M, Trojanowski JQ, Irwin DJ2019Annals of NeurologyNeuroscienceClassifier, Area Quantification,
CCN3/Nephroblastoma Overexpressed Is a Functional Mediator of Prostate Cancer Bone Metastasis That Is Associated with Poor Patient Prognosis Dankner M, Ouellet V, Communal L, Schmitt E, Perkins D, Annis MG, Barrès V, Caron C, Mes-Masson A-M, Saad F, Siegel PM2019The American Journal of PathologyOncologyArea Quantification
Epigenetic regulation of the thioredoxin-interacting protein (TXNIP) gene by hyperglycemia in kidney De Marinis Y, Cai M, Bompada P, Atac D, Kotova O, Johansson ME, Garcia-Vaz E, Gomez MF, Laakso M, Groop L2016Kidney InternationalMetabolismArea Quantification
Evaluation of PD-L1 expression on vortex-isolated circulating tumor cells in metastatic lung cancer Dhar M, Wong J, Che J, Matsumoto M, Grogan T, Elashof D, Garon EB, Goldman JW, Christen ES, Carlo DD, Kulkarni RP2018Scientific ReportsOncology, Immuno-oncologyArea Quantification
Asymmetry of post-mortem neuropathology in behavioural-variant frontotemporal dementia DJ Irwin, CT McMillan, SX Xie, K Rascovsky, VM Van Deerlin, HB Coslett, R Hamilton, G Aguirre, EB Lee, VMY Lee, JQ Trojanowski, M Grossman2017BrainNeuroscienceArea Quantification, Partitions (tiles, margins)
Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosisdo Valle Duraes F, Lafont A, Biebel M, Martin K, Darribat K, Cuttat R, Waldt A, Naumann U, Wieczorek G, Gaulis S, Pfister S, Mertz KD, Li J, Roma G, Warncke M2020JCI InsightImmunologyArea Quantification, Cytonuclear
Co-clinical Analysis of a Genetically Engineered Mouse Model and Human Prostate Cancer Reveals Significance of NKX3.1 Expression for Response to 5α-reductase Inhibition Dutta A, Panja S, Virk RK, Kim JY, Zott R, Cremers S, Golombos DM, Liu D, Mosquera JM, Mostaghel EA, Barbieri CE, Mitrofanova A, Abate-Shen C2017European UrologyOncologyArea Quantification
Effects of advanced age upon astrocyte-specific responses to acute traumatic brain injury in mice Early AN, Gorman AA, Van Eldik LJ, Bachstetter AD, Morganti JM2019bioRxivNeuroscienceArea Quantification
ProNGF is a potential diagnostic biomarker for thyroid cancer Faulkner S, Roselli S, Demont Y, Pundavela J, Choquet G, Leissner P, Oldmeadow C, Attia J, Walker MM, Hondermarck H2016OncotargetOncologyArea Quantification
Imaging breast cancer using hyperpolarized carbon-13 MRIGallagher FA, Woitek R, McLean MA, Gill AB, Garcia RM, Provenzano E, Riemer F, Kaggie J, Chhabra A, Ursprung S, Grist JT, Daniels CJ, Zaccagna F, Laurent M-C, Locke M, Hilborne S, Frary A, Torheim T, Boursnell C, Schiller A, Patterson I, Slough R, Carmo B, Kane J, Biggs H, Harrison E, Deen SS, Patterson A, Lanz T, Kingsbury Z, Ross M, Basu B, Baird R, Lomas DJ, Sala E, Wason J, Rueda OM, Chin S-F, Wilkinson IB, Graves MJ, Abraham JE, Gilbert FJ, Caldas C, Brindle KM2020Proceedings of the National Academy of SciencesOncologyArea Quantification
The neurotrophic tyrosine kinase receptor TrkA and its ligand NGF are increased in squamous cell carcinomas of the lung Gao F, Griffin N, Faulkner S, Rowe CW, Williams L, Roselli S, Thorne RF, Ferdoush A, Jobling P, Walker MM, Hondermarck H2018Scientific ReportsOncologyArea Quantification
Frontotemporal lobar degeneration proteinopathies have disparate microscopic patterns of white and grey matter pathologyGiannini LAA, Peterson C, Ohm D, Xie SX, McMillan CT, Raskovsky K, Massimo L, Suh E, Van Deerlin VM, Wolk DA, Trojanowski JQ, Lee EB, Grossman M, Irwin DJ2021Acta Neuropathologica CommunicationsNeuroscienceArea Quantification
Divergent patterns of TDP‐43 and tau pathologies in primary progressive aphasia Giannini LAA, Xie SX, McMillan CT, Liang M, Williams A, Jester C, Rascovsky K, Wolk DA, Ash S, Lee EB, Trojanowski JQ, Grossman M, Irwin DJ2019Annals of NeurologyNeuroscienceArea Quantification
Empiric Methods to Account for Pre-analytical Variability in Digital Histopathology in Frontotemporal Lobar DegenerationGiannini LAA, Xie SX, Peterson C, Zhou C, Lee EB, Wolk DA, Grossman M, Trojanowski JQ, McMillan CT, Irwin DJ2019Frontiers in NeuroscienceNeuroscienceArea Quantification, Registration, Figure Maker
Conformation-selective tau monoclonal antibodies inhibit tau pathology in primary neurons and a mouse model of Alzheimer’s diseaseGibbons GS, Kim S-J, Wu Q, Riddle DM, Leight SN, Changolkar L, Xu H, Meymand ES, O'Reilly M, Zhang B, Brunden KR, Trojanowski JQ, Lee VMY2020Molecular NeurodegenerationNeuroscienceArea Quantification
TGFβ-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblastsGrauel AL, Nguyen B, Ruddy D, Laszewski T, Schwartz S, Chang J, Chen J, Piquet M, Pelletier M, Yan Z, Kirkpatrick ND, Wu J, deWeck A, Riester M, Hims M, Geyer FC, Wagner J, MacIsaac K, Deeds J, Diwanji R, Jayaraman P, Yu Y, Simmons Q, Weng S, Raza A, Minie B, Dostalek M, Chikkegowda P, Ruda V, Iartchouk O, Chen N, Thierry R, Zhou J, Pruteanu-Malinici I, Fabre C, Engelman JA, Dranoff G, Cremasco V2020Nature CommunicationsOncologyArea Quantification
The novel ATM inhbitior (AZ31) enhances antitumor activity in patient derived xenografts that are resistant to irinotecan montherapy Greene J, Nguyen A, Bagby SM, Jones GN, Tai WM, Quackenbush KS, Schreiber A, Messersmith WA, Devaraj KM, Blatchford P, Eckhardt SG, Cadogan EB, Hughes GD, Smith A, Pitts TM, Arcaroli JJ2018OncotargetOncologyClassifier, Area Quantification, Cytonuclear
Retinoic-acid-orphan-receptor-C inhibition suppresses Th17 cells and induces thymic aberrations Guntermann C, Piaia A, Hamel M-L, Theil D, Rubic-Schneider T, del Rio-Espinola A, Dong L, Billich A, Kaupmann K, Dawson J, Hoegenauer K, Orain D, Hintermann S, Stringer R, Pate DD, Doelemeyer A, Deurinck M, and Schümann J2017JCI InsightOncology, Immuno-oncologyArea Quantification, Cytonuclear
A murine glaucoma model induced by rapid in vivo photopolymerization of hyaluronic acid glycidyl methacrylate Guo C, Qu X, Rangaswamy N, Leehy B, Xiang C, Rice D, Prasanna G2018PLOS OneBiomaterialsArea Quantification
The Dynamics and Turnover of Tau Aggregates in Cultured Cells: Insights into Therapies for Tauopathies Guo JL, Buist A, Soares A, Callaerts K, Calafate S, Stevenaert F, Daniels JP, Zoll BE, Crowe A, Brunden KR, Moechars D, Lee VMY2016The Journal of Biological ChemistryNeuroscienceArea Quantification
Unique pathological tau conformers from Alzheimer's brains transmit tau pathology in nontransgenic mice Guo JL, Narasimhan S, Changolkar L, He Z, Stieber Z, Zhang B, Gathagan RJ, Iba M, McBride JD, Trojanowski JQ, Lee VMY2016Journal of Experimental MedicineNeuroscienceArea Quantification
ANGPTL8/betatrophin does not control pancreatic beta cell expansion Gusarova V, Alexa CA, Na E, Stevis PE, Xin Y, Bonner-Weir S, Cohen JC, Hobbs HH, Murphy AJ, Yancopoulos GD, Gromada J2014CellMetabolismArea Quantification
Recruitment of KRAS downstream target ARL4C to membrane protrusions accelerates pancreatic cancer cell invasionHarada A, Matsumoto S, Yasumizu Y, Akama T, Eguchi H, Kikuchi A2021bioRxivOncologyArea Quantification
Amyloid-β plaques enhance Alzheimer's brain tau-seeded pathologies by facilitating neuritic plaque tau aggregationHe Z, Guo JL, McBride JD, Narasimhan S, Kim H, Changolkar L, Zhang B, Gathagan RJ, Yue C, Dengler C, Stieber A, Nitla M, Coulter DA, Abel T, Brunden KR, Trojanowski JQ, Lee V M-Y2017Nature MedicineNeuroscienceArea Quantification
Transmission of tauopathy strains is independent of their isoform compositionHe Z, McBride JD, Zu, Changolkar L, Kim S, Zhang B, Narasimhan S, Gibbons GS, Kozak M, Schellenberg GD, Trrojanowski JQ, Lee VM-Y2020Nature CommunicationsNeuroscienceArea Quantification
Dendritic Cell Paucity Leads to Dysfunctional Immune Surveillance in Pancreatic CancerHedge S, Krisnawan VE, Herzog BH, Zuo C, Breden MA, Knolhoff BL, Hogg GD, Tang JP, Baer JM, Mpoy C, Lee KB, Alexander KA, Rogers BE, Murphy KM, Hawkins WG, Fields RC, DeSelm CJ, Schwarz JK, DeNardo DG2020Cancer CellOncology, Immuno-oncologyArea Quantification, Cytonuclear, Immune
Characterization of novel conformation-selective α-synuclein antibodies as potential immunotherapeutic agents for Parkinson's diseaseHenderson MX, Covell DJ, Chung C-HY, Pitkin RM, Sandler RM, Decker SC, Riddle DM, Zhang B, Gathagan RJ, James MJ, Trojanowski JQ, Brunden KR, Lee VMY, Luk KC2019Neurobiology of DiseaseNeuroscienceArea Quantification
LLRRK2 inhibition does not impart protection from α-synuclein pathology and neuron death in non-transgenic miceHenderson MX, Sengupta M, McGeary I, Zhang B, Olufemi MF, Brown H, Trojanowski JQ, Lee VMY2019Acta Neuropathologica CommunicationsNeuroscienceArea Quantification, Cytonuclear
Alzheimerís disease tau is a prominent pathology in LRRK2 Parkinsonís disease Henderson MX, Sengupta M, Trojanowski JQ, Lee VMY2019Acta Neuropathologica CommunicationsNeuroscienceArea Quantification
Receptor tyrosine kinase expression and phosphorylation in canine nasal carcinoma Hocker SA, Higginbotham ML, Schermerhorn T, Henningson J2017Research in Veterinary ScienceOncologyArea Quantification, Multiplex IHC
Lenvatinib induces death of human hepatocellular carcinoma cellsharboring an activated FGF signaling pathway through inhibition ofFGFReMAPK cascades Hoshi T, Miyano SW, Watanabe H, Sonobe RMK, Seki Y, Ohta E, Nomoto K, Matsui J, Funahashi Y2019Biochemical and Biophysical Research CommunicationsOncologyArea Quantification
Molecular and functional heterogeneity of cancer associated fibroblasts in high-grade serous ovarian cancer Hussain A, Voisin V, Poon S, Dmytryshyn J ,Richman C, Meens J, Ho VW, Tang KH, Paterson J, Clarke B, Bernardini M, Bader G, Neel B, Ailles L2019bioRxivOncologyClassifier, Area Quantification
Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21Hussain A, Voisin V, Poon S, Karamboulas C, Bui NHB, Meens J, Dmtryshyn J, Ho VW, Tang KH, Paterson J, Clarke BA, Bernardini MQ, Bader GD, Neel BG,4 Ailles LE2020Journal of Experimental MedicineOncologyClassifier, Area Quantification,
Photoacoustic imaging biomarkers for monitoring biophysical changes during nanobubble-mediated radiation treatmentHysi E, Fadhel MN, Wang Y, Sebastian JA, Giles A, Czarnota GJ, Exner AA, Kolios MC2020PhotoacousticsOtherClassifier, Area Quantification, Object Colocalization
Ante mortem CSF tau levels correlate with post mortem tau pathology in FTLD Irwin DJ, Lleó A, Xie SX, McMillan CT, Wolk D, Lee EB, Van Deerlin VM, Shaw LM, Trojanowski JQ, Grossman M2017Annals of NeurologyNeuroscienceArea Quantification
Human cardiac fibroblasts expressing VCAM1 improve heart function in postinfarct heart failure rat models by stimulating lymphangiogenesisIwamiya T, Segnard B-D, Matsuoka Y, Imamura T2020PLOS OneMyologyArea Quantification
Systemic messenger RNA as an etiological treatment for acute intermittent porphyria Jiang L, Berraondo P, Jericó D, Guey LT, Sampedro A, Frassetto A, Benenato KE, Burke K, Santamaría E, Alegre M, Pejenaute A, Kalariya M, Butcher W, Park JS, Zhu X, Sabnis S, Kumarasinghe ES, Salerno T, Kenney M, Lukacs CM, Ávila MA, Martini PGV, Fontanellas A2018Nature MedicineMetabolismArea Quantification
Microbial regulation of enteric eosinophils and its impact on tissue remodeling and Th2 immunity Jimenez-Saiz R, Anipindi VC, Galipeau H, Ellenbogen Y, Chaudhary R, Koenig JF, Gordon ME, Walker TD, Mandur TS, Abed S, Humbles A, Chu DK, Ask K, Verdu EF, Jordana M2019bioRxivImmunology, Infectious DiseaseArea Quantification
Environmental contaminant ammonia triggers epithelial-to-mesenchymal transition-mediated jejunal fibrosis with the disassembly of epithelial cell-cell contacts in chickenJing H, Wang S, Wang Y, Shen N, Gao X-J2020ScienceTotalEnvrtToxicologyArea Quantification
Potential role of M2 TAMs around lymphatic vessels during lymphatic invasion in papillary thyroid carcinomaKabasawa T, Ohe R, Aung NY, Urano Y, Kitaoka T, Tamazawa N, Utsunomiya A, Yamakawa M2021Scientific ReportsOncologyArea Quantification
Neutorphils dominate the immune cell composition in non-small cell lung cancer Kargl J, Busch SE, Yang GHY, Kim K-H, Hanke ML, Metz HE, Hubbard JJ, Lee SM, Madtes DK, McIntosh MW, Houghton AM2017Nature CommunicationsOncologyArea Quantification
Selective imaging of internalized proteopathic α-synuclein seeds in primary neurons reveals mechanistic insight into transmission of synucleinopathies Karpowicz RJ, Haney CM, Mihaila TS, Sandler RM, Petersson EJ, and Lee VM-Y2017Journal of Biological ChemistryNeuroscienceArea Quantification, Cytonuclear
Alzheimer Disease Pathology-Associated Polymorphism in a Complex Variable Number of Tandem Repeat Region Within the MUC6 Gene, Near the AP2A2 GeneKatsumata Y, Fardo DW, Bachstetter AD, Artiushin SC, Wang W-X, Wei A, Brzezinski LJ, Nelson BG, Huang Q, Abner EL, Anderson S, Patel I, Shaw BC, Price DA, Niedowicz DM, Wilcock DW, Jicha GA, Neltner JH, Van Eldik LJ, Estus S, Nelson PT2019Journal of Neuropathology & Experimental NeurologyNeuroscienceArea Quantification, Object Colocalization
DPP9 enzyme activity controls survival of mouse migratory tongue muscle progenitors and its absence leads to neonatal lethality due to suckling defect Kim T, Tafoya E, Chelliah MP, Lekwuttikarn R, Li J, Sarin KY, Teng J2017Developmental BiologyMyologyClassifier, Area Quantification
Tumor Microenvironment in Functional Adrenocortical Adenomas: Immune Cell Infiltration in Cortisol-producing Adrenocortical Adenoma Kitawaki Y, Nakamura Y, Kubota-Nakayama F, YamazakiY, Miki Y, Hata S, Ise K, Kikuchie K, MorimotoR, Satoh F, Sasano H2018Human PathologyOncology, Immuno-oncologyArea Quantification
BMP pathway antagonism by Grem1 regulates epithelial
cell fate in intestinal regeneration
Koppens MAJ, Davis H, Valbuena GN, Mulholland EJ, Nasreddin N, Colombe M, Antanaviciute A, Biswas S, Friedrich M, Lee L, Oxford IBD cohort investigators, Wang LM, Koelzer VH, East JE, Simmons A, Winton DJ, Leedham SJ2021bioRxivGastroenterologyArea Quantification
Connexin-43 and aquaporin-4 are markers of ageing-related tau astrogliopathy (ARTAG)-related astroglial response Kovacs GG, Yousef A, Kaindl S, Lee VM, Trojanowski JQ2017Neuropathology and Applied NeurobiologyNeuroscienceArea Quantification
Age-related pathology after adenoviral overexpression of the leucine-rich repeat kinase 2 in the mouse striatum Kritzingerab A, Ferger B, Gillardon F, Stierstorfer B, Birk G, Kochanek S, Ciossek T2018Neurobiology of AgingNeuroscienceArea Quantification, Object Colocalization, Microglia
Up-Regulation of Iba-1 and GFAP in the Acidic Saline Model of Chronic Widespread Musculoskeletal Pain: A Pilot Study Examining the Relationship Between Gliosis and HyperalgesiaLambert DM, Kumar U, Hafell UO2018Journal of Neuroscience and NeuropharmacologyNeuroscienceArea Quantification, Partitions (tiles, margins)
Characterization of psoriasiform dermatitis induced by systemic injection of interleukin‐23 minicircles in miceLeys L, Wang Y, Paulsboe S, Edelmayer R, Salte K, Wetter J, Namovic M, Phillips L, Dunstan R, Gauvin D, Donnelly-Roberts D, Su Z, Honore P, McGaraughty S2019The Journal of DermatologyDermatologyArea Quantification, Layer Thickness
Tough Composite Hydrogels with High Loading and Local Release of Biological Drugs Li J, Weber E, Guth‐Gundel S, Schuleit M, Kuttler A, Halleux C, Accart N, Doelemeyer A, Basler A, Tigani B, Wuersch K, Fornaro M, Kneissel M, Stafford A, Freedman BR, Mooney DJ2018Advanced Healthcare MaterialsBiomaterialsArea Quantification
IRAK4 mediates colitis-induced tumorigenesis and chemoresistance in colorectal cancerLi Q, Chen Y, Zhang D, Grossman J, Li L, Khurana N, Jiang H, Grierson PM, Herndon J, DeNardo DG, Challen GA, Liu J, Ruzinova MB, Fields RC, Lim K-H2019JCI InsightOncology, Immuno-oncologyArea Quantification
Amylin deposition activates HIF1α and 6-phosphofructo-2-kinase/fructose-2, 6-biphosphatase 3 (PFKFB3) signaling in failing hearts of non-human primatesLiu M, Li N, Qu C, Gao Y, Wu L, Hu LG2021Communications BiologyMetabolismArea Quantification, Cytonuclear
Differential α-synuclein expression contributes to selective vulnerability of hippocampal neuron subpopulations to fibril-induced toxicity Luna E, Decker SC, Riddle DM, Caputo A, Zhang B, Cole T, Caswell C, Xie SX, Lee VMY, Luk KC2018Acta NeuopathologicaNeuroscienceArea Quantification, Cytonuclear
Chronic Intermittent Hypoxia Induces Robust Astrogliosis in an Alzheimer's Disease-Relevant Mouse Model Macheda T, Roberts K, Lyons DN, Higgins E, Ritter KJ, Lin A-L, Alilain WJ, Bachstetter AD2018NeuroscienceNeuroscienceArea Quantification
Dysregulated expression but redundant function of the long non-coding RNA HOTAIR in diabetic kidney disease Majumder S, Hadden MJ, Thieme K, Batchu SN, Niveditha D, Chowdhury S, Yerra VG, Advani SL, Bowskill BB, Liu Y, Vakili H, Alghamdi TA, White KE, Geldenhuys L, Siddiqi FS, Advani A2019DiabetologiaMetabolismArea Quantification
Evaluation of the brain-penetrant microtubule-stabilizing agent, dictyostatin, in the PS19 tau transgenic mouse model of tauopathy Makani V, Zhang B, Han H, Yao Y, Lassalas P, Lou K, Paterson I, Lee VMY, Trojanowski JQ, Ballatore C, Smith AB, Brunden KR2016Acta Neuropatholgica CommunicationsNeuroscienceArea Quantification
Targeted drug delivery via caveolae-associated protein PV1 improves lung fibrosis Marchetti GM, Burwell TJ, Peterson NC, Cann JA, Hanna RN, Li Q, Ongstad EL, Boyd JT, Kennedy MA, Zhao W, Rickert KW, Grimsby JS, Dall’Acqua WF, Wu H, Tsui P, Borrok MJ, Gupta R2019Communications BiologyFibrosisArea Quantification
CNS-accessible inhibitor of glucosylceramide synthase for substrate reduction therapy of neuronopathic Gaucher disease Marshall J, Sun Y, Bangari DS, Budman E, Park H, Nietupski JB, Allaire A, Cromwell MA, Wang B, Grabowski GA, Leonard JP, Cheng SH2016Molecular TherapyNeuroscienceArea Quantification
Persistence of inflammatory phenotype in residual psoriatic plaques in patients on effective biologic therapy: Residual Psoriatic Plaques After Treatment Mashiko S, Edelmayer RM, Bi Y, Olson LM, Wetter JB, Wang J, Maari C, Proulx ES-C, Kaimal V, Li X, Salte K, Garcet S, Kannan AK, Huang SM, Cao X, Liu Z, Krueger JG, Sarfati M, Bissonnette R, Smith KM2019Journal of Investigative DermatologyImmunology, DermatologyArea Quantification
Cholinergic receptors on intestine cells of Ascaris suum and activation of nAChRs by levamisoleMcHugh M, Williams P, Verma S, Powell-Coffman JA, Robertson AP, Martin RJ2020International Journal for Parasitology: Drugs and Drug ResistanceGastroenterology, Infectious DiseaseArea Quantification
Adult onset pan-neuronal human tau tubulin kinase 1 expression causes severe cerebellar neurodegeneration in miceMcMillan P, Wheeler J, Gatlin RE, Taylor L, Strovas T, Baum M, Bird TD, Latimer C, Keene CD, Kraemer BC, Liachko NF2020Acta Neuropathologica CommunicationsNeuroscienceArea Quantification
In Situ Temporospatial Characterization of the Glial Response to Prion Infection Michael AV, Greenlee JJ, Harm TA, Moore SJ, Zhang M, Lind MS, Greenlee MHW, Smith JD2019Veterinary PathologyImmunology, Neuroscience, Infectious DiseaseArea Quantification
Spatial immune profiling of the colorectal tumor microenvironment predicts good outcome in stage II patientsNearchou IP, Gwyther BM, Georgiakakis ECT, Gavriel CG, Kajiwara Y, Ueno H, Harrison DJ, Caie PD2020Digital MedicineImmuno-oncologyClassifier, Area Quantification, Spatial Analysis
Exposure to maternal obesity programs sex differences in pancreatic islets of the offspring in mice Nicholas LM, Nagao M, Kusinski LC, Fernandez-Twinn DS, Eliasson L, Ozanne SE2019DiabetologiaMetabolismArea Quantification
Glucagon Receptor Blockade With a Human Antibody Normalizes Blood Glucose in Diabetic Mice and Monkeys Okamoto H, Cavino K, Na E, Krumm E, Kim SY, Cheng X, Murphy AJ, Yancopoulos GD, Gromada J2015EndocrinologyMetabolismArea Quantification
Angptl4 does not control hyperglucagonemia or α-cell hyperplasia following glucagon receptor inhibition Okamoto H, Cavino K, Na E, Krumm E, Kim SY, Stevis PE, Harp J, Murphy AJ, Yancopoulos GD, Gromada J2017Proceedings of the National Academy of SciencesMetabolismArea Quantification
Glucagon receptor inhibition normalizes blood glucose in severe insulin-resistant mice Okamoto H, Kim J, Aglione JP, Lee J, Cavino K, Na E, Rafique A, Kim JH, Harp J, Valenzuela DM, Yancopoulos GD, Murphy AJ, Gromada J2017Proceedings of the National Academy of SciencesMetabolismArea Quantification
Histological characterization of aldosterone-producing adrenocortical adenomas with different somatic mutations Ono Y, Yamazaki Y, Omata K, Else T, Tomlins SA, Rhayem Y, Williams TA, Reincke M, Carling T, Monticone S, Mulatero P, Beuschlein F, Ito S, Satoh F, Rainey WE, Sasano H2019The Journal of Clinical Endocrinology & MetabolismOncologyClassifier, Area Quantification
Cysteinyl leukotriene receptor 1 facilitates tumorigenesis in a mouse model of colitis-associated colon cancerOsman J, Savari S, Chandrashekar NK, Bellamkonda K, Souglas D, Sjolander A2017OncotargetOncology, ImmunologyClassifier, Area Quantification
Cellular milieu imparts distinct pathological α-synuclein strains in α-synucleinopathies Peng C, Gathagan RJ, Covell DJ, Medellin C, Stieber A, Robinson JL, Zhang B, Pitkin RM, Olufemi MF, Luk KC, Trojanowski JQ, Lee VM-Y2018NatureNeuroscienceArea Quantification
Leptin, BMI, and a Metabolic Gene Expression Signature Associated with Clinical Outcome to VEGF Inhibition in Colorectal Cancer Pommier AJC, Farren M, Patel B, Wappett M, Michopoulos F, Smith NR, Kendrew J, Frith J, Huby R, Eberlein C, Campbell H, Womack C, Smith PD, Robertson J, Morgan S, Critchlow SE, Barry ST2016Cell MetabolismOncology, Metabolism, GastroenterologyArea Quantification
Epithelial to mesenchymal plasticity and differential response to therapies in pancreatic ductal adenocarcinomaPorter RL, Magnus NKC, Thapar V, Morris R, Szabolcs A, Neyaz A, Kulkarni AS, Tai E, Chougule A, Hillis A, Golczer G, Guo H, Yamada T, Kurokawa T, Yashaswini C, Ligorio M, Vo KD, Nieman L, Liss AS, Deshpande V, Lawrence MS, Maheswaran S, Fernandez-Del Castillo C, Hong TS, Ryan DP, O’Dwyer PJ, Drebin JA, Ferrone CR, Haber DA, Ting DT2019Proceedings of the National Academy of SciencesOncologyArea Quantification
Plant-based vaccines for oral delivery of type 1 diabetes-related autoantigens: Evaluating oral tolerance mechanisms and disease prevention in NOD mice Posgai AL, Wasserfall CH, Kwon K-C, Daniell H, Schatz DA, Atkinson MA2017Scientific ReportsMetabolismArea Quantification
Nerve fibers infiltrate the tumor microenvironment and are associated with nerve growth factor production and lymph node invasion in breast cancer Pundavela J, Roselli S, Faulkner S, Attia J, Scott RJ, Thorne RF, Forbes JF, Bradshaw RA, Walker MM, Jobling P, Hondermarck H2015Molecular OncologyOncology, NeuroscienceArea Quantification
The action of β-hydroxybutyrate on the growth, metabolism and global histone H3 acetylation of spontaneous mouse mammary tumours: evidence of a β-hydroxybutyrate paradox Rodrigues LM, Uribe-Lewis S, Madhu B, Honess DJ, Stubbs M, Griffiths JR2017Cancer & MetabolismOncology, MetabolismArea Quantification, Cytonuclear
11β hydroxysteroid dehydrogenase 1: a new marker for predicting response to immune-checkpoint blockade therapy in non-small-cell lung carcinomaSaito R, Miki Y, Abe T, Miyauchi E, Abe J, Nanamiya R, Inoue C, Sato I, Sasano H2020British Journal of CancerImmuno-oncologyArea Quantification
Expression of protein disulfide isomerase family members correlates with tumor progression and patient survival in ovarian cancer Samanta S, Tamura S, Dubeau L, Mhawech-Fauceglia P, Miyagi Y, Kato H, Lieberman R, Buckanovich RJ, Lin YG, Neamati N2017OncotargetOncologyArea Quantification
Clinicopathological significance of endoplasmic reticulum stress proteins in ovarian carcinomaSamanta S, Tamura S, Dubeau L, Mhawech-Fauceglia P, Miyagi Y, Kato H, Lieberman R, Buckanovich RJ, Lin YG, Neamati N2020Scientific ReportsOncologyArea Quantification
Dystrophic microglia are associated with neurodegenerative disease and not healthy aging in the human brainShahidehpour RK, Higdon RE, Crawford NG, Neltner JH, Ighodaro ET, Patel E, Price D, Nelson PT, Bachstetter AD2021Neurobiology of AgingNeuroscienceArea Quantification
Inhibition of Hedgehog signaling alters fibroblast composition in pancreatic cancer Steele NG, Biffi G, Kemp SB, Zhang Y, Drouillard D, Syu L-J, Hao Y, Oni TE, Brosnan E, Elyada E, Doshi A, Hansma C, Espinoza C, Abbas A, The S, Irizarry-Negron VM, Halbrook CJ, Franks N, Hoffman M, Brown KL, Carpenter ES, Nwosu ZC, Johnson C, Lima F, Anderson MA, Park Y, Crawford HC, Lyssiotis CA, Frankel TF, Rao A, Bednar F, Dlugosz AA, Preall J, Tuveson DA, Allen B, di Magliano MP2021Clinical Cancer ResearchOncologyArea Quantification
IL‐36 receptor antagonistic antibodies inhibit inflammatory responses in preclinical models of psoriasiform dermatitis Su Z, Paulsboe S, Wetter J, Salte K, Kannan A, Mathew S, Horowitz A, Gerstein C, Namovic M, Todorović V, Seagal J, Edelmayer RM, Viner M, Rinaldi L, Zhou L, Leys L, Huang S, Wang L, Sadhukhan R, Honore P, McGaraughty S, Scott VE2019Experimental DermatologyDermatologyArea Quantification, Cytonuclear
FK506-binding protein 13 expression is upregulated in interstitial lung disease and correlated with clinical severity: a potentially protective role Tat V, Ayaub EA, Ayoub A, Vierhout M, Naiel S, Padwal MK, Abed S, Mekhael O, Tandon K, Revill SD, Yousof T, Bellaye PS, Kolb PS, Dvorkin-Gheva A, Naqvi A, Cutz JC , Hambly N, Kato J, Vaughan M, Moss J, Kolb MRJ, Ask K2019bioRxivImmunology, FibrosisArea Quantification
Disease Progression and Pharmacological Intervention in a Nutrient-Deficient Rat Model of Nonalcoholic Steatohepatitis Tølbøl KS, Stierstorfer B, Rippmann JF, Veidal SS, Rigbolt KTG, Schönberger T, Gillum MP, Hansen HH, Vrang N, Jelsing J, Feigh M, Broermann A2018Digestive Diseases and SciencesMetabolismArea Quantification
Ad26 vaccine protects against SARS-CoV-2 severe clinical disease in hamstersTostanoski LH, Wegmann F, Martinot AJ, Loos C, McMahan K, Mercado NB, Yu J, Chan CN, Bondoc S, Starke CE, Nekorchuk M, Busman-Sahay K, Piedra-Mora C, Wrijil LM, Ducat S, Custers J, Atyeo C, Fischinger S, Burke JS, Feldman J, Hauser BM, Caradonna TM, Bondzie EA, Dagotto G, Gebre MS, Jacob-Dolan C, Lin Z, Mahrokhian SH, Nampanya F, Nityanandam R, Pessaint L, Porto M, ALi V, Benetiene D, Tevi K, Andersen H, Lewis MG, Schmidt AG, Lauffenburger DA, Alter G, Estes JD, Schuitemaker H, Zahn R, Barouch DH2020Nature MedicineInfectious DiseaseArea Quantification, Multiplex IHC
A CD3-bispecific molecule targeting P-cadherin demonstrates T cell-mediated regression of established solid tumors in mice TS Fisher, AT Hooper, J Lucas, TH Clark, AK Rohner, B Peano, MW Elliott, K Tsaparikos, H Wang, J Golas, M Gavriil, N Haddish-Berhane, L Tchistiakova, H-P Gerber, AR Root, C May2018Cancer Immunology, ImmunotherapyOncology, Immuno-oncologyArea Quantification
Solid-state NMR structure of a pathogenic fibril of full-length human [alpha]-synuclein Tuttle MD, Comellas G, Nieuwkoop AJ, Covell DJ, Berthold DA, Kloepper KD, Courtney JM, Kim JK, Barclay AM, Kendall A, Wan W, Stubbs G, Schwieters CD, Lee VMY, George JM, Rienstra CM2016Structural & Molecular BiologyNeuroscienceArea Quantification
Formoterol, a β2-adrenoreceptor agonist, induces mitochondrial biogenesis and promotes cognitive recovery after traumatic brain injuryVekaria HJ, Hubbard WB, Scholpa NE, Spry ML, Gooch JL, Prince SJ, Schnellmann Sullivan PG2020Neurobiology of DiseaseNeuroscienceArea Quantification
Persistence of Pancreatic Insulin mRNA Expression and Proinsulin Protein in Type 1 Diabetes Pancreata Wasserfall C, Nick HS, Campbell-Thompson M, Beachy D, Haataja L, Kusmartseva I, Posgai A, Beery M, Rhodes C, Bonifacio E, Arvan P, Atkinson M2017Cell MetabolismMetabolismArea Quantification
Evaluation of Peritumoral Fibrosis in Metastatic Colorectal Adenocarcinoma to the Liver Using Digital Image Analysis Waters KM, Cottrell TR, Besharati S, Zhu Q, Anders RA2019American Journal of Clinical PathologyOncologyArea Quantification, Partitions (tiles, margins)
Synergistic targeted inhibition of MEK and dual PI3K/mTOR diminishes viability and inhibits tumor growth of canine melanoma underscoring its utility as a preclinical model for human mucosal melanoma Wei B-R, Michael HT, Hasley CHC, Peer CJ, Adhikari A, Dwyer JE, Hoover SB, El Meskini R, Kozlov S, Ohler ZW, Figg WD, Merlino G, Simpson RM2016Pigment Cell & Melanoma ResearchOncologyArea Quantification
Tumor Cell Subtypes Based on the Intracellular Hormonal Activity in KCNJ5-Mutated Aldosterone-Producing Adenoma Yamazaki Y, Omata K, Tezuka Y, Ono Y, Morimoto R, Adachi Y, Ise K, Nakamura Y, Gomez-Sanchez CE, Shibahara Y, Kitamoto T, Nishikawa T, Ito S, Satoh F, Sasano H2018HypertensionOncologyArea Quantification, Cytonuclear
A phase 2 study of GVAX colon vaccine with cyclophosphamide and pembrolizumab in patients with mismatch repair proficient advanced colorectal cancerYarchoan M, Huang C-Y, Zhu Q, Ferguson AK, Durham JN, Anders RA, Thompson ED, Rozich NS, Thomas DL, Nauroth JM, Rodriguez C, Osipov A, De Jesus-Acosta A, Le DT, Murphy AG, Laheru D, Donehower RC, Jaffee EM, Zheng L, Azad NS2019Cancer MedicineImmuno-oncologyArea Quantification, Partitions (tiles, margins)
Neuron loss and degeneration in the progression of TDP-43 in frontotemporal lobar degeneration Yousef A, Robinson JL, Irwin DJ, Byrne MD, Kwong LK, Lee EB, Xu Y, Xie SX, Rennert L, Suh ER, Van Deerlin VM, Grossman M, Lee VM-Y, Trojanowski JQ2017Acta Neuropathologica CommunicationsArea Quantification, Cytonuclear
Ossabaw Pigs With a PCSK9 Gain‐of‐Function Mutation Develop Accelerated Coronary Atherosclerotic Lesions: A Novel Model for Preclinical Studies Yuan F, Guo L, Park K-H, Woollard JR, Taek‐Geun K, Jiang K, Melkamu T, Zang B, Smith SL, Fahrenkrug SC, Kolodgie FD, Lerman A, Virmani R, Lerman LO, Carlson DF2018Journal of the American Heart AssociationMyologyArea Quantification
A brain-penetrant triazolopyrimidine enhances microtubule-stability, reduces axonal dysfunction and decreases tau pathology in a mouse tauopathy model. Zhang B, Yao Y, Cornec A-S, Oukoloff K, James MJ, Koivula P, Trojanowski JQ, Smith AB III, Lee VM-Y, Ballatore C, Brunden KR2018Molecular NeurodegenerationNeuroscienceArea Quantification

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