Nuclear v9 algorithm

Manufactured by Leica

Sourced in United States

The Nuclear v9 algorithm is a computational tool designed for image processing and analysis. It is a core function that performs numerical calculations and mathematical operations on digital image data. The algorithm enables the processing and manipulation of visual information, facilitating tasks such as image enhancement, segmentation, and feature extraction. The specific details and intended use cases for this product are not available.

Automatically generated - may contain errors

Lab products found in correlation

Imagescope software, by Leica (2 mentions) Aperio imagescope program, by Leica (1 mentions) Aperio scanscope cs slide scanner, by Leica (1 mentions) Imagescope viewer, by Leica (1 mentions) Scanscope at2 scanner, by Leica (1 mentions)

Spelling variants of this product

Aperio nuclear v9 algorithm (2 citations)

6 protocols using nuclear v9 algorithm

Immunohistochemical Scoring Algorithm

Check if the same lab product or an alternative is used in the 5 most similar protocols

The expression of all markers was measured in manually annotated regions using the Nuclear v9 algorithm (Aperio Technologies), with minor adjustments for stain optical density and nuclear shape. The intensity score (1+ = weak positive, 2+ = moderately positive, and 3+ = strong positive), and the percentage of positive cells for each score was used to calculate the H-score using the formula

H-score = [{(% at 1 +)}^{*} 1] + [{(% at 2 +)}^{*} 2] + [{(% at 3 +)}^{*} 3] .

Swahari V., Nakamura A., Baran-Gale J., Garcia I., Crowther A.J., Sons R., Gershon T.R., Hammond S., Sethupathy P, & Deshmukh M. (2015). Essential Function of Dicer in Resolving DNA Damage in the Rapidly Dividing Cells of the Developing and Malignant Cerebellum. Cell reports, 14(2), 216-224.

+ Open protocol

+ Expand

Quantitative Protein Expression Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

TMA samples containing more than 500 malignant cells were considered for evaluation. Scanned images of the stained slides were viewed using Aperio ImageScope program (version 11.2.0.782; Aperio Technologies, Vista, CA, USA) at 20x objective magni cation. Automated digital image analysis was performed using Genie classi er and Nuclear v9 algorithm (Aperio Technologies). The percentages of stained cells and intensities of staining were estimated in the cytoplasm for MLKL and PELI1 and in the nucleus for RIPK3, p53, gH2AX, ATM, Chk2, BRCA1, and ERCC1 by two pathologists (H.J.J. and L.K.). The evaluators were blinded to each patient's results for the clinical and pathological variables and survival status.
H-score method was applied to evaluate protein expression. The percentage of tumor cells with positive cytoplasmic or nucleus staining on each TMA core was calculated and assigned a score of either 0 (0% stained tumor cells), 0.1 (1-9%), 0.5 (10-49%), or 1 (≥ 50%). The staining intensity was assigned a score of either 0 (weakest intensity), 1, 2, or 3 (strongest intensity). Each H-score was obtained by multiplying the proportion by the staining intensity. The median values of all mean H-scores were used as the cut-off values for the classi cation of the expression of the nine proteins as either "low" or "high" (Supplementary Fig. 2).

Lim J.H., Oh S., Kim L., Suh Y.J., Ha Y., Kim J.S., Kim H.J., Park M.H., Kim Y.S., Cho Y., Kwak S.M., Lee H.L., Kim Y., & Ryu J. (2020). Low-level expression of necroptosis factors indicative of a poor prognosis of squamous cell carcinoma subtype of non-small-cell lung cancer.

+ Open protocol

+ Expand

Quantitative Immunohistochemical Analysis of DNA Mismatch Repair Proteins

Check if the same lab product or an alternative is used in the 5 most similar protocols

The immunohistochemical slides were subsequently scanned into high-resolution images using the Aperio Scanscope CS Slide Scanner (Aperio Technologies Inc, Vista, CA). All digital images obtained in .svs format were visualized using the ImageScope software (Aperio Technologies Inc., Vista, CA). MSH2 and MSH6 nuclear staining was analyzed using the Nuclear V9 algorithm (Aperio Technologies Inc, Vista, CA) with the following input parameters: averaging radius: 0.9; curvature threshold: 2.5; lower threshold: 0; upper threshold: 230; minimum nuclear size: 22; maximum nuclear size: 165; minimum roundness: 0.3; minimum compactness: 0.1; minimum elongation: 0.2; clear area objective: 240; and an intensity threshold ranging from 0 to 230, in which strong staining was considered from 0 to 185 and weak staining was from 185 to 230. At least 1000 cells were quantified in 10 hotspot areas of each case and the percentage of positive cells was determined.

Wagner V.P., Webber L.P., Salvadori G., Meurer L., Fonseca F.P., Castilho R.M., Squarize C.H., Vargas P.A, & Martins M.D. (2016). Overexpression of MutSα Complex Proteins Predicts Poor Prognosis in Oral Squamous Cell Carcinoma. Medicine, 95(22), e3725.

+ Open protocol

+ Expand

Automated Analysis of IHC Staining

Check if the same lab product or an alternative is used in the 5 most similar protocols

Automated digital image analysis of IHC staining (Figure 1) was performed using a Genie classifier and the Nuclear v9 algorithm (for ER and PR) or Membrane v9 algorithm (for HER2; Aperio Technologies, Vista, CA), and is described in more detail in Supplementary Materials and Methods.
To validate automated analyses, study pathologists (JG, HH, TK) carried out manual reviews of IHC staining within a training set of TMAs. For ER and PR, individual cores were classified as negative (<1% positive), borderline (≥1% and <10%) or positive (≥10%). For HER2, individual cores were classified as negative (0/1+), positive (3+) or equivocal (2+) [21 (link)]. Using a 10% threshold to define ER and PR status, agreement between automated and manual scoring was 89% for ER and 91% for PR (Supplementary Table S1). After excluding cores with equivocal HER2 (2+) status in either the TMA or clinical record (n=63), HER2 status agreement between automated and manual scoring was 93%. As expected, agreement was slightly lower with additional categories [ER and PR status as negative (<1%), borderline (1–10%) or positive (≥10%), HER2 status as negative (0/1+), equivocal (2+) or positive (3+), Supplementary Table S1].

Allott E.H., Cohen S.M., Geradts J., Sun X., Khoury T., Bshara W., Zirpoli G.R., Miller C.R., Hwang H., Thorne L.B., O’Connor S., Tse C.K., Bell M.B., Hu Z., Li Y., Kirk E.L., Bethea T.N., Perou C.M., Palmer J.R., Ambrosone C.B., Olshan A.F, & Troester M.A. (2015). Performance of three biomarker immunohistochemistry for intrinsic breast cancer subtyping in the AMBER consortium. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 25(3), 470-478.

+ Open protocol

+ Expand

Quantifying ERα and PR Expression in Fallopian Tubes

Check if the same lab product or an alternative is used in the 5 most similar protocols

ERα- and PR-immunostained slides were scanned at a magnification of 400× (resolution of 0.25 μm/pixel) using the ScanScope AT2 scanner (Leica Microsystems, Wetzlar, Germany). The obtained digital images of the slides were analyzed using the ImageScope viewer (Version 11.2.0.780; Aperio Technologies, Vista, CA, USA). Immunoexpression of ERα and PR in the glandular epithelium and the stroma of the ampulla and isthmus of the fallopian tubes was expressed as a percentage of ERα- and PR-immunopositive cells using automatic computer analysis. For this assessment, a nuclear v9 algorithm (version 9.1; Aperio Technologies, Vista, CA, USA) was applied. Analyzed areas were manually determined. Using the algorithm, the percentage of cells with ERα-positive and PR-positive immunostaining was independently counted in 40 random fields in each group with an average area of 0.4 mm².

Brodowska A., Grabowska M., Bittel K., Ciećwież S., Brodowski J., Szczuko M., Szydłowska I, & Piasecka M. (2021). Estrogen and Progesterone Receptor Immunoexpression in Fallopian Tubes among Postmenopausal Women Based on Time since the Last Menstrual Period. International Journal of Environmental Research and Public Health, 18(17), 9195.

+ Open protocol

+ Expand

ATRX Immunohistochemistry in Glioblastoma

Check if the same lab product or an alternative is used in the 5 most similar protocols

Immunohistochemistry was performed to detect ATRX loss using antibodies against ATRX (rabbit polyclonal, 1:600; Sigma-Aldrich, St. Louis, MO, USA). Sections from known mutation-positive and immunoreactive GBM tumors were used as positive controls. Sections incubated with normal rabbit serum instead of the primary antibody were used as negative controls. ATRX was scored as negative if staining loss was observed in > 90% of tumor cells. Immunoreactivity was assessed using the Aperio ImageScope software with the Nuclear v9 algorithm (Aperio Technologies, Vista, CA, USA).

Kim S., Chowdhury T., Yu H.J., Kahng J.Y., Lee C.E., Choi S.A., Kim K.M., Kang H., Lee J.H., Lee S.T., Won J.K., Kim K.H., Kim M.S., Lee J.Y., Kim J.W., Kim Y.H., Kim T.M., Choi S.H., Phi J.H., Shin Y.K., Ku J.L., Lee S., Yun H., Lee H., Kim D., Kim K., Hur J.K., Park S.H., Kim S.K, & Park C.K. (2022). The telomere maintenance mechanism spectrum and its dynamics in gliomas. Genome Medicine, 14, 88.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!