Indica
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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 Author Year Journal
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
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
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
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
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
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
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
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
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
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
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
Glucagon receptor inhibition normalizes blood glucose in severe insulin-resistant mice Okamotoa H, Cavinoa K, Na E, Krumm E, Kim SY, Cheng X, Murphy AJ, Yancopoulos GD, Gromada J 2017 Proceedings of the National Academy of Sciences
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
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
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
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
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
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
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
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
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
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
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
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 George D.Yancopoulos, John Rudge, Israel Lowy, Hsin Chieh Lin, Douglas MacDonald, 2016 Pigment Cell & Melanoma Research
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
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
Glucagon Receptor Blockade With a Human Antibody Normalizes Blood Glucose in Diabetic Mice and Monkeys 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 2015 Endocrinology
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
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

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.