Nuance software

Manufactured by PerkinElmer

Sourced in United States

Nuance software is a digital imaging and analysis tool designed to facilitate the processing, visualization, and interpretation of scientific data. It provides a comprehensive suite of tools for image acquisition, enhancement, and analysis, enabling researchers to extract valuable insights from their experimental data.

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Lab products found in correlation

Inform software, by PerkinElmer (3 mentions) Vectra slide scanner, by PerkinElmer (2 mentions) Microtome, by Leica (1 mentions) Rat anti mouse cd68, by Bio-Rad (1 mentions) Diamond anti fading medium, by Thermo Fisher Scientific (1 mentions) Dm4000b, by Leica (1 mentions) ι carrageenan, by Merck Group (1 mentions)

Close spelling variants of this product

Nuance software version 3.02 (5 citations) Nuance imaging software (2 citations) Nuance Image Analysis software (2 citations) Nuance Multispectral Image camera and software (2 citations) Nuance Imaging Analysis software (2 citations)

8 protocols using nuance software

Multiplex Immunohistochemical Analysis

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Analysis using the Vectra system was performed as described in previous studies [5 (link),13 (link)]. Stained slides were loaded into the Vectra slide scanner (PerkinElmer, Waltham, MA, USA), and a scanning protocol was produced. Eight-bit Nuance multispectral image cubes were created with the ×20 lens. Nuance software (version 3.0.0; PerkinElmer) was then used to build the spectral library (Fig. 1). Three control slides with 1 chromogen (3,3′-diaminobenzidine, hematoxylin, and Warp Red) were scanned, and spectral curves were defined to unmix signals (Fig. 2).
Images were imported using inForm software (version 1.4; PerkinElmer). Initially, 18% of cores from the TMA were used to set up an algorithm for differentiation, assuring 97% acceptable tissue segmentation [5 (link)]. Target signals were then quantified in selected tissues and cellular compartments of interest (Fig. 3). For HIF1α and HIF2α, nuclear expression was used in the analysis because these transcription factors are active when present in the nuclear compartment. For Ki-67, the percentage of cells with positive nuclear staining was used because Ki-67 is a cellular marker for proliferation located in nuclei. For CRP, the global cellular expression was used in the analysis. Core images with less than 5% epithelial component, significant folding, or loss of tissue were excluded.

Abel E.J., Bauman T.M., Weiker M., Shi F., Downs T.M., Jarrard D.F, & Huang W. (2014). Analysis and validation of tissue biomarkers for renal cell carcinoma using automated high-throughput evaluation of protein expression. Human pathology, 45(5), 1092-1099.

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Multiplex Immunofluorescence Analysis of NKTL

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For the multiplex immunofluorescence (MIF), a cohort of patient samples were retrieved from the archives of the Department of Pathology, National University Hospital of patients diagnosed with NKTL between 1992 and 2017. The patient study group and preparation of samples for MIF are further described in online supplemental methods.
Image acquisition and analysis were done with the Vectra V.2 multispectral automated imaging system (PerkinElmer) and in Form V.2.0 image analysis software. Nuance software (PerkinElmer) was employed to build the spectral libraries for the chromogens (Opal 520, Opal 690 and DAPI). These chromogen signature profiles were later used to spectrally unmix and quantitate CD3 and CD38 staining intensity, with appropriate regions for analysis chosen by two pathologists. For each case, four images containing at least 10 000 cells were analyzed. The absolute optical density of each chromogen indicating the intensity of each antibody was obtained for every image and normalized against respective positive cut-offs.

Mustafa N., Nee A.H., Chooi J.Y., Toh S.H., Chung T.H., Selvarajan V., Fan S., Ng S.B., Poon M., Chan E., Lee J., Chee Y.L., Jeyasekharan A.D., Zhou L., Yang J, & Chng W.J. (2021). Determinants of response to daratumumab in Epstein-Barr virus-positive natural killer and T-cell lymphoma. Journal for Immunotherapy of Cancer, 9(7), e002123.

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Multispectral Imaging for Chromogen and Fluorochrome Analysis

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Multispectral images were captured using a Vectra® multispectral microscope and camera (PerkinElmer, Waltham, MA) at 400X magnification (8 bits/pixel depth) from 420 nm-720 nm at 20 nm wavelength intervals (brightfield mode) or 10 nm wavelength intervals (fluorescence mode). Nuance® software (PerkinElmer, Waltham, MA) was used to spectrally unmix the image cubes into individual channels corresponding to hematoxylin, DAB, and the fluorochromes (Alexa Fluor 488, Alexa Fluor 647, Cy3). Unmixing was based on the pure spectra of the respective chromogens and fluorochromes.

Padmanabhan R.K., Somasundar V.H., Griffith S.D., Zhu J., Samoyedny D., Tan K.S., Hu J., Liao X., Carin L., Yoon S.S., Flaherty K.T., DiPaola R.S., Heitjan D.F., Lal P., Feldman M.D., Roysam B, & Lee W.M. (2014). An Active Learning Approach for Rapid Characterization of Endothelial Cells in Human Tumors. PLoS ONE, 9(3), e90495.

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Multiplex Immunofluorescence Quantification

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Data acquisition and image analysis was performed using the Vectra slide scanner (PerkinElmer, Waltham, MA), Nuance software (PerkinElmer) and inForm software (PerkinElmer), as previously described [16 (link), 17 (link)]. CD147 expression and E-cadherin expression were used to identify and segment epithelial cell plasma membrane, and hematoxylin was used to segment nuclei (Additional file 1: Figure S1). CD147 and E-cadherin expression were then quantified in the membrane and cytoplasm of the epithelium. Cores with significant folding or <5 % epithelium were eliminated from analysis. The average mean OD of duplicate cores was used for analysis if both cores were available and sufficient for analysis.

Bauman T.M., Ewald J.A., Huang W, & Ricke W.A. (2015). CD147 expression predicts biochemical recurrence after prostatectomy independent of histologic and pathologic features. BMC Cancer, 15, 549.

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Histological and Immunofluorescent Analysis of CFA-Induced Inflammation

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Male and female mice were sacrificed after 40 days post CFA injection, and both of the right and left paws were harvested. Tissues were prepared for histology with hematoxylin and eosin (H&E) and immunostaining. The excised tissue and organ samples were fixed in 4% PFA solution, embedded into paraffin, and cut into 10 μm sections using microtome (Leica, Buffalo Grove, IL). The sections were stained with H&E according to standard protocols. For immunostaining; non-specific binding was blocked with Dako serum free protein for 15 min at room temperature. Rat anti-mouse CD68 (Bio-Rad, Hercules, CA) (1/200 dilution in DPBS/0.1% BSA/0.05% Tween-20) and goat anti-mouse COX-2 antibodies (Novus, Centennial, CO) (at 1/50 dilution in PBS/0.1% BSA/0.05% Tween-20) were added overnight at 4 °C followed by a secondary antibody, anti-rat-Alexa 488 and anti-goat- Alexa 594 (Invitrogen, Grand Island, NY) (1/300 dilution in PBS/0.1% BSA/0.05% Tween-20) for 1 h at RT. After washing in DPBS/0.05% Tween-20, coverslips were mounted using Diamond anti-fading medium (Invitrogen, Grand Island, NY). Immunofluorescence staining was monitored using an Olympus BX63 fluorescence microscope with a multispectral camera by CRI (Perkin Elmer) and Nuance software.

Liu L., Karagoz H., Herneisey M., Zor F., Komatsu T., Loftus S., Janjic B.M., Gorantla V.S, & Janjic J.M. (2020). Sex Differences Revealed in a Mouse CFA Inflammation Model with Macrophage Targeted Nanotheranostics. Theranostics, 10(4), 1694-1707.

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Multispectral Immunohistochemical Analysis

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A PerkinElmer Vectra (Hopkinton, MA, USA) multispectral slide scanner was used to capture image files at 10 nm intervals across the visible range (440 to 700 nm) and at × 200 magnification from which grey-scale distribution maps for CD3, FOXP3 and CD69 positivity for each core were derived by spectral un-mixing as previously described (Mansfield et al, 2008 ). Using these distribution maps, two multispectral image analyses were performed. Firstly Inform software (PerkinElmer, Hopkinton, MA, USA) was used to identify single positive CD3⁺ cells and double positive CD3/FOXP3⁺ and CD3/CD69⁺ cells, and the number and density of these measured in each core. Secondly Nuance software (PerkinElmer) was used to separately identify positive regions and their centroid co-ordinates for CD3, FOXP3 and CD69 positive staining, as required for HID analysis (Rose et al, 2013 (link)). The results of these two analyses were exported to Excel (Microsoft Corporation, Redmond, WA, USA) for use in Kaplan–Meier (K–M) survival and HID analyses, respectively, as detailed below.

Nelson L.S., Mansfield J.R., Lloyd R., Oguejiofor K., Salih Z., Menasce L.P., Linton K.M., Rose C.J, & Byers R.J. (2015). Automated prognostic pattern detection shows favourable diffuse pattern of FOXP3+ Tregs in follicular lymphoma. British Journal of Cancer, 113(8), 1197-1205.

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Fluorescence-based pH Measurement in Cerebrospinal Fluid

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The fluorescence dye SNARF-4F 5-(and-6)-carboxylic acid (SNARF) was purchased from ThermoFisher Scientific. The fluorescence microscope consists of a light source (PhotoFluorII NIR, 89 North, Burlington, VT, USA), a microscope (Leica DM4000B, Leica Microsystems, Wetzlar, Germany) with Nuance EX Fluorescence detector and Nuance Software (PerkinElmer, Hopkinton, MA, USA). Two filter sets for green (515–560 nm) and red (620–660 nm) excitation light were used to illuminate the sample. The emitted light was detected above the excitation wavelength. Multispectral imaging cube sets were acquired in 1 nm steps using automatic exposure times [20 (link)]. The intensities at I(609 nm) and I(625 nm) at green excitation light and I(679 nm) at red excitation light were read out of the cube and saved as images, which were loaded in the origin software and handled as matrices. The ratio of intensities was calculated as follows.

ratio = \frac{[I {(609 nm)}^{gr} - I {(679 nm)}^{red}]}{I {(625 nm)}^{gr}}

The pH was calculated with a sigmoidal calibration curve (Figure S1). The calculated pH is shown in Figure 3B. SNARF (21 µg) was dissolved in 200 µL CSF, 23 mm² (1.5 mg) Tabotamp^® were placed at a cavity slide and wetted with 50 µL of dye solution.

Leisz S., Trutschel M.L., Mäder K., Scheller C., Strauss C, & Simmermacher S. (2020). Tabotamp®, Respectively, Surgicel®, Increases the Cell Death of Neuronal and Glial Cells In Vitro. Materials, 13(11), 2453.

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Visualizing Viral Particle Localization

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SHIN-3 DSR cells (1 × 10⁷) were injected IP into nude mice. AF488 VLP (100µg) were administered 14 days later by IP injection. Tissues from animals treated with AF488 VLPs were harvested after 2 hr. To test inhibition of binding, AF488 VLP were pre-incubated with 100µl of 1% ι-carrageenan (Sigma) for 1 hr prior to injection. At the designated time points, the animals were euthanized, and the small intestine was removed from each animal and placed in a wheel formation on a black background for imaging. A Maestro device outfitted with a multispectral camera (PerkinElmer, Waltham, MA) with blue and green excitation filters paired with a 515-nm and a 580-nm long-pass emission filter, respectively, was used to obtain images from 500 nm to 900 nm in 10-nm wavelength increments. A spectral unmixing algorithm was applied to the composite images to determine the intensity and location of infection. Images were acquired, processed and analyzed using Nuance software (Perkin Elmer) and Image J (NIH, Bethesda, MD). After imaging, tissues were embedded in tissue freezing media (EMS), frozen, and 6µm sections were made and fixed to the slides for 10 min in −20°C ethanol (100%), then mounted and imaged as described above.

Kines R.C., Cerio R.J., Roberts J.N., Thompson C.D., de Los Pinos E., Lowy D.R, & Schiller J.T. (2015). Human papillomavirus capsids preferentially bind and infect tumor cells. International journal of cancer. Journal international du cancer, 138(4), 901-911.

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