Area Quantification Brightfield
Area Quantification
Product Overview
Area Quantification IHC quantifies up to five brightfield stains on a per area rather than per cell or object basis. It is a flexible alternative for analyzing tissues where cell structure cannot be readily identified or where tissue area-based outputs are more reliable or meaningful measure. Area Quantification quantifies and reports stain positive area, average stain optical density for each stain, binned positivity based on optical density (0, 1+, 2+ and 3+), and area of colocalization (when multiple stains are analyzed).
In the first example shown above, an intensity markup is generated such that weak positive pixels (1+) are highlighted in yellow, moderate positive pixels (2+) are highlighted in orange, and strong positive pixels (3+) are in red. In the second example, a co-localization markup is generated such that brown positive pixels are red, pink positive pixels are green, and co-localized pixels are yellow.
Note that the Indica Labs’ Area Quantification 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 Brightfield
Area Quantification IHC quantifies up to five brightfield stains on a per area rather than per cell or object basis. It is a flexible alternative for analyzing tissues where cell structure cannot be readily identified or where tissue area-based outputs are more reliable or meaningful measure. Area Quantification quantifies and reports stain positive area, average stain optical density for each stain, binned positivity based on optical density (0, 1+, 2+ and 3+), and area of colocalization (when multiple stains are analyzed).
In the first example shown above, an intensity markup is generated such that weak positive pixels (1+) are highlighted in yellow, moderate positive pixels (2+) are highlighted in orange, and strong positive pixels (3+) are in red. In the second example, a co-localization markup is generated such that brown positive pixels are red, pink positive pixels are green, and co-localized pixels are yellow.
Note that the Indica Labs’ Area Quantification 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!
| Title | Authors | Year | Journal | Application | HALO Modules |
|---|---|---|---|---|---|
| Anti-NKG2A mAb Is a Checkpoint Inhibitor that Promotes Anti-tumor Immunity by Unleashing Both T and NK Cells | Andre ́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 E | 2018 | Cell | Oncology, Immuno-oncology | Area 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 Hudson | 2017 | The American Journal of Pathology | Oncology | Classifier, 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 JP | 2018 | Nature Medicine | Myology | Area 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 MT | 2017 | Parasitology Research | Infectious Disease | Area 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 M | 2017 | Journal of Biological Chemistry | Myology | Area 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 RA | 2017 | Environmental Health Perspectives | Metabolism | Area Quantification |
| Stem cell–derived CAR T cells traffic to HIV reservoirs in macaques | Barber-Axthelm IM, Barber-Axthelm V, Sze KY, Zhen A, Suryawanshi GW, Chen ISY, Zack JA, Kitchen SG, Kiem H-P, Peterson CW | 2021 | JCI Insight | Immunology, Infectious Disease | Area 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 JA | 2019 | Pigment Cell & Melanoma Research | Dermatology | Area Quantification |
| Tuning of delta-protocadherin adhesion through combinatorial | Bisogni AJ, Ghazanfar S, Williams EO, Marsh HM, Yang JYH, Lin DM | 2018 | eLife | Neuroscience | Area 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 fraction | Bustamante M, Garate‐Carrillo A, Ito BR, Garcia R, Carson N, Ceballos G, Ramirez‐Sanchez I, Omens J, Villarreal F | 2019 | The Journal of Physiology | Myology | Area Quantification, Laer Thickness |
| Epithelial-mesenchymal transition of absorptive enterocytes and depletion of Peyer's patch M cells after PEDV infection | Chen Y-M, Helm ET, Groeltz-Thrush, Gabler NK, Burrough ER | 2020 | Virology | Immunology | Area Quantification |
| Glucagon contibutes to liver zonation | Cheng X, Kim SK, Okamoto H, Xin Y, Yancopoulos GD, Murphy AJ, Gromada J | 2018 | Proceedings of the National Academy of Sciences | Metabolism | Area Quantification |
| Impact of Preanalytical Factors During Histology Processing on Section Suitability for Digital Image Analysis | Chlipala EA, Butters M, Brous M, Fortin JS, Archuletta R, Copeland K, Bolon B | 2020 | Toxicologic Pathology | Toxicology | Area Quantification, Cytonuclear |
| Methacrylic Acid Copolymer Coating Enhances Constructive Remodeling of Polypropylene Mesh by Increasing the Vascular Response | Coindre VF, Carleton MM, Sefton MV | 2019 | Advanced Healthcare Materials | Biomaterials | Area 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 DJ | 2019 | Annals of Neurology | Neuroscience | Classifier, 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 PM | 2019 | The American Journal of Pathology | Oncology | Area 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 L | 2016 | Kidney International | Metabolism | Area 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 RP | 2018 | Scientific Reports | Oncology, Immuno-oncology | Area 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 Grossman | 2017 | Brain | Neuroscience | Area Quantification, Partitions (tiles, margins) |
| Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis | do 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 M | 2020 | JCI Insight | Immunology | Area 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 C | 2017 | European Urology | Oncology | Area 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 JM | 2019 | bioRxiv | Neuroscience | Area 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 H | 2016 | Oncotarget | Oncology | Area Quantification |
| Imaging breast cancer using hyperpolarized carbon-13 MRI | Gallagher 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 KM | 2020 | Proceedings of the National Academy of Sciences | Oncology | Area 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 H | 2018 | Scientific Reports | Oncology | Area Quantification |
| Frontotemporal lobar degeneration proteinopathies have disparate microscopic patterns of white and grey matter pathology | Giannini 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 DJ | 2021 | Acta Neuropathologica Communications | Neuroscience | Area 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 DJ | 2019 | Annals of Neurology | Neuroscience | Area Quantification |
| Empiric Methods to Account for Pre-analytical Variability in Digital Histopathology in Frontotemporal Lobar Degeneration | Giannini LAA, Xie SX, Peterson C, Zhou C, Lee EB, Wolk DA, Grossman M, Trojanowski JQ, McMillan CT, Irwin DJ | 2019 | Frontiers in Neuroscience | Neuroscience | Area Quantification, Registration, Figure Maker |
| Conformation-selective tau monoclonal antibodies inhibit tau pathology in primary neurons and a mouse model of Alzheimer’s disease | Gibbons 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 VMY | 2020 | Molecular Neurodegeneration | Neuroscience | Area Quantification |
| TGFβ-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts | Grauel 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 V | 2020 | Nature Communications | Oncology | Area 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 JJ | 2018 | Oncotarget | Oncology | Classifier, 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 J | 2017 | JCI Insight | Oncology, Immuno-oncology | Area 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 G | 2018 | PLOS One | Biomaterials | Area 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 VMY | 2016 | The Journal of Biological Chemistry | Neuroscience | Area 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 VMY | 2016 | Journal of Experimental Medicine | Neuroscience | Area 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 J | 2014 | Cell | Metabolism | Area Quantification |
| Recruitment of KRAS downstream target ARL4C to membrane protrusions accelerates pancreatic cancer cell invasion | Harada A, Matsumoto S, Yasumizu Y, Akama T, Eguchi H, Kikuchi A | 2021 | bioRxiv | Oncology | Area Quantification |
| Amyloid-β plaques enhance Alzheimer's brain tau-seeded pathologies by facilitating neuritic plaque tau aggregation | He 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-Y | 2017 | Nature Medicine | Neuroscience | Area Quantification |
| Transmission of tauopathy strains is independent of their isoform composition | He Z, McBride JD, Zu, Changolkar L, Kim S, Zhang B, Narasimhan S, Gibbons GS, Kozak M, Schellenberg GD, Trrojanowski JQ, Lee VM-Y | 2020 | Nature Communications | Neuroscience | Area Quantification |
| Dendritic Cell Paucity Leads to Dysfunctional Immune Surveillance in Pancreatic Cancer | Hedge 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 DG | 2020 | Cancer Cell | Oncology, Immuno-oncology | Area Quantification, Cytonuclear, Immune |
| Characterization of novel conformation-selective α-synuclein antibodies as potential immunotherapeutic agents for Parkinson's disease | Henderson 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 KC | 2019 | Neurobiology of Disease | Neuroscience | Area Quantification |
| LLRRK2 inhibition does not impart protection from α-synuclein pathology and neuron death in non-transgenic mice | Henderson MX, Sengupta M, McGeary I, Zhang B, Olufemi MF, Brown H, Trojanowski JQ, Lee VMY | 2019 | Acta Neuropathologica Communications | Neuroscience | Area Quantification, Cytonuclear |
| Alzheimerís disease tau is a prominent pathology in LRRK2 Parkinsonís disease | Henderson MX, Sengupta M, Trojanowski JQ, Lee VMY | 2019 | Acta Neuropathologica Communications | Neuroscience | Area Quantification |
| Receptor tyrosine kinase expression and phosphorylation in canine nasal carcinoma | Hocker SA, Higginbotham ML, Schermerhorn T, Henningson J | 2017 | Research in Veterinary Science | Oncology | Area 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 Y | 2019 | Biochemical and Biophysical Research Communications | Oncology | Area 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 L | 2019 | bioRxiv | Oncology | Classifier, Area Quantification |
| Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21 | Hussain 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 LE | 2020 | Journal of Experimental Medicine | Oncology | Classifier, Area Quantification, |
| Photoacoustic imaging biomarkers for monitoring biophysical changes during nanobubble-mediated radiation treatment | Hysi E, Fadhel MN, Wang Y, Sebastian JA, Giles A, Czarnota GJ, Exner AA, Kolios MC | 2020 | Photoacoustics | Other | Classifier, 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 M | 2017 | Annals of Neurology | Neuroscience | Area Quantification |
| Human cardiac fibroblasts expressing VCAM1 improve heart function in postinfarct heart failure rat models by stimulating lymphangiogenesis | Iwamiya T, Segnard B-D, Matsuoka Y, Imamura T | 2020 | PLOS One | Myology | Area 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 A | 2018 | Nature Medicine | Metabolism | Area 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 M | 2019 | bioRxiv | Immunology, Infectious Disease | Area Quantification |
| Environmental contaminant ammonia triggers epithelial-to-mesenchymal transition-mediated jejunal fibrosis with the disassembly of epithelial cell-cell contacts in chicken | Jing H, Wang S, Wang Y, Shen N, Gao X-J | 2020 | ScienceTotalEnvrt | Toxicology | Area Quantification |
| Potential role of M2 TAMs around lymphatic vessels during lymphatic invasion in papillary thyroid carcinoma | Kabasawa T, Ohe R, Aung NY, Urano Y, Kitaoka T, Tamazawa N, Utsunomiya A, Yamakawa M | 2021 | Scientific Reports | Oncology | Area 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 AM | 2017 | Nature Communications | Oncology | Area 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-Y | 2017 | Journal of Biological Chemistry | Neuroscience | Area Quantification, Cytonuclear |
| Alzheimer Disease Pathology-Associated Polymorphism in a Complex Variable Number of Tandem Repeat Region Within the MUC6 Gene, Near the AP2A2 Gene | Katsumata 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 PT | 2019 | Journal of Neuropathology & Experimental Neurology | Neuroscience | Area 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 J | 2017 | Developmental Biology | Myology | Classifier, 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 H | 2018 | Human Pathology | Oncology, Immuno-oncology | Area 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 SJ | 2021 | bioRxiv | Gastroenterology | Area 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 JQ | 2017 | Neuropathology and Applied Neurobiology | Neuroscience | Area 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 T | 2018 | Neurobiology of Aging | Neuroscience | Area 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 Hyperalgesia | Lambert DM, Kumar U, Hafell UO | 2018 | Journal of Neuroscience and Neuropharmacology | Neuroscience | Area Quantification, Partitions (tiles, margins) |
| Characterization of psoriasiform dermatitis induced by systemic injection of interleukin‐23 minicircles in mice | Leys 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 S | 2019 | The Journal of Dermatology | Dermatology | Area 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 DJ | 2018 | Advanced Healthcare Materials | Biomaterials | Area Quantification |
| IRAK4 mediates colitis-induced tumorigenesis and chemoresistance in colorectal cancer | Li 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-H | 2019 | JCI Insight | Oncology, Immuno-oncology | Area Quantification |
| Amylin deposition activates HIF1α and 6-phosphofructo-2-kinase/fructose-2, 6-biphosphatase 3 (PFKFB3) signaling in failing hearts of non-human primates | Liu M, Li N, Qu C, Gao Y, Wu L, Hu LG | 2021 | Communications Biology | Metabolism | Area 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 KC | 2018 | Acta Neuopathologica | Neuroscience | Area 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 AD | 2018 | Neuroscience | Neuroscience | Area 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 A | 2019 | Diabetologia | Metabolism | Area 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 KR | 2016 | Acta Neuropatholgica Communications | Neuroscience | Area 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 R | 2019 | Communications Biology | Fibrosis | Area 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 SH | 2016 | Molecular Therapy | Neuroscience | Area 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 KM | 2019 | Journal of Investigative Dermatology | Immunology, Dermatology | Area Quantification |
| Cholinergic receptors on intestine cells of Ascaris suum and activation of nAChRs by levamisole | McHugh M, Williams P, Verma S, Powell-Coffman JA, Robertson AP, Martin RJ | 2020 | International Journal for Parasitology: Drugs and Drug Resistance | Gastroenterology, Infectious Disease | Area Quantification |
| Adult onset pan-neuronal human tau tubulin kinase 1 expression causes severe cerebellar neurodegeneration in mice | McMillan P, Wheeler J, Gatlin RE, Taylor L, Strovas T, Baum M, Bird TD, Latimer C, Keene CD, Kraemer BC, Liachko NF | 2020 | Acta Neuropathologica Communications | Neuroscience | Area 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 JD | 2019 | Veterinary Pathology | Immunology, Neuroscience, Infectious Disease | Area Quantification |
| Spatial immune profiling of the colorectal tumor microenvironment predicts good outcome in stage II patients | Nearchou IP, Gwyther BM, Georgiakakis ECT, Gavriel CG, Kajiwara Y, Ueno H, Harrison DJ, Caie PD | 2020 | Digital Medicine | Immuno-oncology | Classifier, 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 SE | 2019 | Diabetologia | Metabolism | Area 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 J | 2015 | Endocrinology | Metabolism | Area 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 J | 2017 | Proceedings of the National Academy of Sciences | Metabolism | Area 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 J | 2017 | Proceedings of the National Academy of Sciences | Metabolism | Area 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 H | 2019 | The Journal of Clinical Endocrinology & Metabolism | Oncology | Classifier, Area Quantification |
| Cysteinyl leukotriene receptor 1 facilitates tumorigenesis in a mouse model of colitis-associated colon cancer | Osman J, Savari S, Chandrashekar NK, Bellamkonda K, Souglas D, Sjolander A | 2017 | Oncotarget | Oncology, Immunology | Classifier, 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-Y | 2018 | Nature | Neuroscience | Area 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 ST | 2016 | Cell Metabolism | Oncology, Metabolism, Gastroenterology | Area Quantification |
| Epithelial to mesenchymal plasticity and differential response to therapies in pancreatic ductal adenocarcinoma | Porter 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 DT | 2019 | Proceedings of the National Academy of Sciences | Oncology | Area 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 MA | 2017 | Scientific Reports | Metabolism | Area 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 H | 2015 | Molecular Oncology | Oncology, Neuroscience | Area 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 JR | 2017 | Cancer & Metabolism | Oncology, Metabolism | Area Quantification, Cytonuclear |
| 11β hydroxysteroid dehydrogenase 1: a new marker for predicting response to immune-checkpoint blockade therapy in non-small-cell lung carcinoma | Saito R, Miki Y, Abe T, Miyauchi E, Abe J, Nanamiya R, Inoue C, Sato I, Sasano H | 2020 | British Journal of Cancer | Immuno-oncology | Area 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 N | 2017 | Oncotarget | Oncology | Area Quantification |
| Clinicopathological significance of endoplasmic reticulum stress proteins in ovarian carcinoma | Samanta S, Tamura S, Dubeau L, Mhawech-Fauceglia P, Miyagi Y, Kato H, Lieberman R, Buckanovich RJ, Lin YG, Neamati N | 2020 | Scientific Reports | Oncology | Area Quantification |
| Dystrophic microglia are associated with neurodegenerative disease and not healthy aging in the human brain | Shahidehpour RK, Higdon RE, Crawford NG, Neltner JH, Ighodaro ET, Patel E, Price D, Nelson PT, Bachstetter AD | 2021 | Neurobiology of Aging | Neuroscience | Area 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 MP | 2021 | Clinical Cancer Research | Oncology | Area 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 VE | 2019 | Experimental Dermatology | Dermatology | Area 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 K | 2019 | bioRxiv | Immunology, Fibrosis | Area 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 A | 2018 | Digestive Diseases and Sciences | Metabolism | Area Quantification |
| Ad26 vaccine protects against SARS-CoV-2 severe clinical disease in hamsters | Tostanoski 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 DH | 2020 | Nature Medicine | Infectious Disease | Area 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 May | 2018 | Cancer Immunology, Immunotherapy | Oncology, Immuno-oncology | Area 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 CM | 2016 | Structural & Molecular Biology | Neuroscience | Area Quantification |
| Formoterol, a β2-adrenoreceptor agonist, induces mitochondrial biogenesis and promotes cognitive recovery after traumatic brain injury | Vekaria HJ, Hubbard WB, Scholpa NE, Spry ML, Gooch JL, Prince SJ, Schnellmann Sullivan PG | 2020 | Neurobiology of Disease | Neuroscience | Area 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 M | 2017 | Cell Metabolism | Metabolism | Area 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 RA | 2019 | American Journal of Clinical Pathology | Oncology | Area 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 RM | 2016 | Pigment Cell & Melanoma Research | Oncology | Area 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 H | 2018 | Hypertension | Oncology | Area Quantification, Cytonuclear |
| A phase 2 study of GVAX colon vaccine with cyclophosphamide and pembrolizumab in patients with mismatch repair proficient advanced colorectal cancer | Yarchoan 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 NS | 2019 | Cancer Medicine | Immuno-oncology | Area 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 JQ | 2017 | Acta Neuropathologica Communications | Area 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 DF | 2018 | Journal of the American Heart Association | Myology | Area 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 KR | 2018 | Molecular Neurodegeneration | Neuroscience | Area Quantification |
| Exploring transcriptional regulators Ref-1 and STAT3 as therapeutic targets in malignant peripheral nerve sheath tumours | Gampala S, Shah F, Zhang C, Rhodes SD, Babb O, Grimard M, Wireman RS, Rad E, Calver B, Bai R-Y, Staedtke V, Hulsey EL, Saadatzadeh MR, Pollok KE, Tong Y, Smith AE, Clapp DW, Tee AR, Kelley MR, Fishel ML | 2021 | British Journal of Cancer | Oncology | Area Quantification, Cytonuclear |
| An extended release GLP-1 analogue increases α-synuclein accumulation in a mouse model of prodromal Parkinson's disease | Bergkvist L, Johnson ME, Mercado G, Steiner JA, Meyerdick L, Schulz E, Madaj Z, Ma J, Becker K, Li Y, Brudin P | 2021 | Experimental Neurology | Neuroscience | Area Quantification |
| Promyelocytic leukemia protein promotes the phenotypic switch of smooth muscle cells in atherosclerotic plaques of human coronary arteries | Karle W, Becker S, Stenzel P, Knosalla C, Siegel G, Baum O, Zakrzewicz A, Berkholz J | 2021 | Clinical Science | Myology | Area Quantification |
| Age-associated expression of p21and p53 during human wound healing | Chia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L | 2021 | Aging Cell | Dermatology | Area Quantification, ISH/FISH, Multiplex IHC |
| Inhibition of STAT3 augments antitumor efficacy of anti-CTLA-4 treatment against prostate cancer | Witt K, Evans-Axelsson S, Lundqvist A, Johansson M, Bjartell A, Hellsten R | 2021 | Cancer Immunology, Immunotherapy | Immuno-oncology | Area Quantification, Multiplex IHC |
Use the form below to upload up to three images for us to analyze using HALO. If the form does not display, please click here.