Olyvia software

Manufactured by Olympus

Sourced in Japan, United States

OlyVIA software is a digital imaging software developed by Olympus for use with their microscopes and imaging systems. It provides tools for image capture, processing, and analysis.

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Lab products found in correlation

Axio observer z1, by Zeiss (6 mentions) Vs120 virtual slide microscope, by Olympus (5 mentions) Vs120 microscope, by Olympus (4 mentions) Vs120, by Olympus (3 mentions) Benchmark xt, by Roche (3 mentions) Alexa fluor 568, by Thermo Fisher Scientific (2 mentions) 5 bromo 4 chloro 3 indolyl phosphate nitro blue tetrazolium bcip nbt substrate, by Roche (2 mentions) Vs200, by Olympus (2 mentions) Bx61vs light microscope, by Olympus (2 mentions) Hematoxylin and bluing reagent, by Roche (2 mentions) Cell conditioning 1, by Roche (2 mentions) Ultraview universal dab detection kit, by Roche (2 mentions) Vs 110 microscope, by Olympus (2 mentions) Bx ucb hardware vs120 slide scanner, by Olympus (2 mentions) Vs120 digital slide scanner, by Olympus (2 mentions) Vs120 slide scanner, by Olympus (2 mentions) Bx ucb, by Olympus (2 mentions) Zen software, by Zeiss (2 mentions) Lsm800 confocal microscope, by Zeiss (2 mentions) Histofine simple stain max po, by Nichirei Biosciences (1 mentions)

Close spelling variants of this product

OlyVIA (45 citations) OlyVIA analysis software (3 citations) VS120 slide scanner Olyvia software (2 citations)

66 protocols using olyvia software

Immunofluorescence Staining of MT-9 Cells

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Cultured MT-9 cells at subconfulency were fixed by periodate-lysine-paraformaldehyde (PLP) fixative [40 (link)]. Chamber slide was permeabilized with 0.03% Triton X-100 in phosphate-buffered saline (PBS) after PLP-fixation and immunolabeled by A3 (1:1000: TransGenic, Inc., Kobe, Japan) for 1 h at RT. The visualization of specific antibody binding was performed with anti-mouse IgG secondary antibody conjugated with Alexa Fluor® 568 (Thermo Fisher Scientific Inc., Waltham, MA, USA). These chamber slides were coverslipped with Fluoro-KEEPER Antifade Reagent with 4′,6-diamino-2-phenylindole (DAPI) (Nacalai Tesque Inc., Kyoto, Japan) for nuclear staining. Slides were captured by VS120 Virtual Slide Microscope (Olympus Corporation, Tokyo, Japan) and analyzed using Olympus OlyVIA software (Olympus Corporation, Tokyo, Japan).

Katou-Ichikawa C., Nishina H., Tanaka M., Takenaka S., Izawa T., Kuwamura M, & Yamate J. (2020). Participation of Somatic Stem Cells, Labeled by a Unique Antibody (A3) Recognizing Both N-glycan and Peptide, to Hair Follicle Cycle and Cutaneous Wound Healing in Rats. International Journal of Molecular Sciences, 21(11), 3806.

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Immunohistochemical Staining Protocol

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The tissue sections were used for immunolabeling with the primary antibodies, which are shown in Table 1. The bound antibodies were detected with horse radish peroxidase-conjugated anti-rabbit secondary antibody (Histofine Simple stain MAX-PO; Nichirei Bioscience Inc., Tokyo, Japan) and 3,3′-diaminobenzidine (DAB) substrate kit (Vector Laboratories, Burlingame, CA, USA) as chromogen. For double-immunofluorescence of A3 with other antibodies, sections were incubated with Alexa Fluor® 488-labeled or Alexa Fluor® 568-labeled secondary antibodies against mouse IgG (1:1000; Thermo Fisher Scientific Inc., Waltham, MA, USA) for A3 or were incubated with Alexa Fluor® 568-labeled secondary antibody against goat IgG (1:1000; Thermo Fisher Scientific Inc., Waltham, MA, USA) for CD34. These immunofluorescence sections were covered by a mounding medium with DAPI (VECTASHIELD®; Vector Laboratories Inc., Burlingame, CA, USA) for nuclear staining. Slides were scanned using VS120 Virtual Slide Microscope (Olympus Corporation, Tokyo, Japan) and analyzed using Olympus OlyVIA software (Olympus Corporation, Tokyo, Japan).

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Brain Slice Gallyas Staining and Imaging

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A total of 35 brain slices were obtained from 15 samples for our study. To ensure anatomical diversity, at least two slices were taken per sample, with each slice being separated in depth by 1 mm. These slices had a thickness of 50 μm and were mounted onto gelatin-coated slides. Gallyas staining protocol, as described by Pistorio (2 (link)), was then employed to process the samples. Modifications were made to the impregnation and bleaching time to accommodate the increased thickness of the samples.
Following the staining process, the samples were captured in brightfield mode using a 10 × objective (NA=0.4) and an RGB camera. We utilized the VS-120 slide scanner designed for 75 × 25 mm² slides for this purpose. The exposure time was set at 1.73 ms, and the pixel size was 0.7 μm with a 1 × 1 mm² FOV. For wider samples, imaging was conducted using the BZ-X microscope under similar settings. The resulting images can be opened in Olympus Olyvia software and exported as TIFF images for further processing.

Cheng S., Chang S., Li Y., Novoseltseva A., Lin S., Wu Y., Zhu J., McKee A.C., Rosene D.L., Wang H., Bigio I.J., Boas D.A, & Tian L. (2024). Enhanced Multiscale Human Brain Imaging by Semi-supervised Digital Staining and Serial Sectioning Optical Coherence Tomography. Research Square.

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In Situ Hybridization Visualization of Molecular Markers

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Single-label in situ hybridization was performed as described previously^{48 (link)}. Briefly, whole brains were fixed in 4% PFA and embedded in paraffin. Serial coronal sections of 10 μm thickness were cut and hybridized with the above-mentioned ptger4b or npba probe, which was labeled with DIG using DIG RNA Labeling Mix and T7 RNA polymerase (Roche Diagnostics). Hybridization signals were visualized using an alkaline phosphatase-conjugated anti-DIG antibody (RRID: AB_514497; Roche Diagnostics) and 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium (BCIP/NBT) substrate (Roche Diagnostics). Color development was allowed to proceed overnight (for analysis of ptger4b expression) or was stopped within 15 min to avoid saturation (for analysis of npba expression). Brain nuclei were identified using the medaka brain atlas⁵⁰. For quantification of npba expression in FeSP neurons, images were acquired with a virtual slide microscope (VS120; Olympus, Tokyo, Japan) and the total area of npba expression signal in the PMm/PMg was calculated using Olyvia software (Olympus).

Fleming T., Kikuchi Y., Nakajo M., Tachizawa M., Inazumi T., Tsuchiya S., Sugimoto Y., Saito D., Suyama M., Ohkawa Y., Baba T., Morohashi K.I, & Okubo K. (2022). Prostaglandin E2 receptor Ptger4b regulates female-specific peptidergic neurons and female sexual receptivity in medaka. Communications Biology, 5, 1215.

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Ca2+ Signaling Assay in Cells

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Cells were seeded into 384-well assay plates (Greiner Bio-One, 788096) and loaded with the Ca²⁺ indicator Fluo-8 AM (AAT Bioquest, 21081-5) in imaging buffer (1x Hanks Balanced Salt Solution with 10 mM HEPES, pH adjusted to 7.4 with NaOH) for 30 minutes at room temperature. Prior to the start of the experiment, a 20-second baseline fluorescence was recorded, then 50 μM Ogerin, 5 μM Dihydro-testosterone or 50 μM estrogen was added and the recording continued for 2 minutes. After the experiment, at least 100 cells were selected for analysis. The intracellular Ca²⁺ concentration was determined by measuring the fluorescence intensity at 488 nm under various conditions. Images were acquired at 1 frame/s. Region of interest representing individual cells were picked and data analyzed in OlyVia software (Olympus) and exported for further analysis (16 (link)).

Ye S., Zhu Y., Zhong D., Song X., Li J., Xiao F., Huang Z., Zhang W., Wu M., Zhang K., Xiang F.L, & Xu J. (2023). G protein-coupled receptor GPR68 inhibits lymphocyte infiltration and contributes to gender-dependent melanoma growth. Frontiers in Oncology, 13, 1202750.

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Quantifying Neuronal Subpopulations in Mouse Brain

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Images were obtained using a slide scanner microscope (Olympus VS200, Tokyo, Japan) coupled with a VS-264C digital camera. The Olympus OLyVIA software (Olympus) and the Fiji programme (Schindelin et al., 2012 (link)) were used to process the images. The stereotaxic atlas of the mouse brain (Paxinos and Franklin, 2001 ) and Allen Brain Atlas (Allen Institute for Brain Science, 2018 ) were used to identify different nuclei and structures.
Finally, we verified our semiquantitative description of the staining of the area occupied by SCGN-positive cell somata in each nucleus (showed in Table 1) with the Fiji threshold tool (Schindelin et al., 2012 (link)). In addition, some coronal diagrams based on Paxinos and Franklin (2001) with the relative number of positive somata were done for a better understanding of our results (Figure 8).

Téllez de Meneses P.G., Pérez-Revuelta L., Canal-Alonso Á., Hernández-Pérez C., Cocho T., Valero J., Weruaga E., Díaz D, & Alonso J.R. (2023). Immunohistochemical distribution of secretagogin in the mouse brain. Frontiers in Neuroanatomy, 17, 1224342.

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IFNε Expression Detection in Uteri

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Uteri from IL-15-CFP reporter mice were fixed in 10% neutral buffered formalin and embedded in paraffin. Four µm sections were cut and deparaffinized routinely. Heat-induced epitope retrieval (HIER) was performed in citrate buffer (10 mM trisodium citrate, pH 6.0) under pressure using a Biocare decloaking chamber (Biocare; 5 min, 110 °C). To detect IFNε protein, sections were labeled with mouse anti-IFNε (3 μg/mL; generated in-house (Fung et al, 2013 (link))), biotinylated anti-mouse IgG secondary antibody (Table EV1), followed by AF594-labeled Streptavidin (Invitrogen). Background staining was prevented using goat serum (Vector Laboratories). CFP expression was detected with AF488-labeled anti-GFP. Slides were counterstained with 4’,6-diamidine-2’-phenylindole dihydrochloride (DAPI; Molecular Probes) and coverslipped with Fluorescence mounting medium (Agilent). Slides were scanned at 20x magnification using a VS120 Virtual Slide Microscope (Olympus) and analyzed with OlyVIA software (Olympus).

Mayall J.R., Horvat J.C., Mangan N.E., Chevalier A., McCarthy H., Hampsey D., Donovan C., Brown A.C., Matthews A.Y., de Weerd N.A., de Geus E.D., Starkey M.R., Kim R.Y., Daly K., Goggins B.J., Keely S., Maltby S., Baldwin R., Foster P.S., Boyle M.J., Tanwar P.S., Huntington N.D., Hertzog P.J, & Hansbro P.M. (2024). Interferon-epsilon is a novel regulator of NK cell responses in the uterus. EMBO Molecular Medicine, 16(2), 267-293.

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Quantifying Fos-positive Neurons in Mouse Brains

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Sixty min after i.c.v. infusion, mice were euthanized with 7% chloral hydrate and perfused with saline followed by 4% paraformaldehyde in phosphate buffered saline (PBS, pH 7.4). Brains were post fixed in 4% paraformaldehyde/30% sucrose in PBS at 4°C overnight. Coronal brain sections (40 μm) were cut, stored at 4°C for up to one week in PBS containing 0.02% sodium azide, washed in 0.1 M PBS, preincubated in blocking buffer (PBS + 0.2 % triton X-100 + 10% normal horse serum (NHS)) for 2 h at room temperature, and incubated with antibody to Fos (1:2000, Cell Signaling, #5348) in 2% NHS blocking buffer for 48 h at 4°C. After washing in PBS, tissue was incubated for 4 h with donkey anti-rabbit Alexa Fluor 488 antibody (1:500 in PBS + 2% NHS blocking buffer, ThermoFisher Scientific #A31556). Fos was visualized by fluorescence microscopy with Olyvia software (Olympus Life Sciences). A blinded individual counted the Fos-positive neurons using Image J software (NIH). Display images were adjusted for brightness and contrast. Brain anatomy was defined using (Franklin and Paxinos, 2007 ).
Data are reported as mean ± SEM. Significance (two-tailed p < 0.05) was determined by t-test or ANOVA followed by post hoc Holm-Sidak multiple comparison tests.

Carlin J.L., Jain S., Duroux R., Suresh R.R., Xiao C., Auchampach J.A., Jacobson K.A., Gavrilova O, & Reitman M.L. (2018). Activation of adenosine A2A or A2B receptors causes hypothermia in mice. Neuropharmacology, 139, 268-278.

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Quantifying CD8+ T Cells in Tumor Tissue

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In total, 0.8×10⁶ tumor cells were subcutaneously injected into C57BL/6 mice. After 14 days, tumor tissues were dissected, fixed in 4% paraformaldehyde for 24 h, and dehydrated in 30% sucrose for 48 h. For tissue section staining, tissues were embedded in Optimal Cutting Temperature (OCT) compound, frozen, and cryo-sectioned (15–20 microns). Sections were permeabilized for 30 min in PBS with 0.1% Triton X-100 (PBST) and blocked for 1 h in PBS with 3% BSA. To stain for CD8⁺ T cells, rabbit anti-mouse CD8a (Abcam, ab217344, clone: EPR21769, dilution: 1:500) was used as the primary antibody, and AF647-donkey anti-rabbit IgG (Jackson Immuno Research, 711-605-152, clone: 30-F11, dilution: 1:500) was used as the secondary antibody. Stained tissue sections were imaged on a Zeiss LSM800 confocal microscope. Microscopy data were analyzed using OlyVIA software (OLYMPUS).

Cui Y., Miao Y., Cao L., Guo L., Cui Y., Yan C., Zeng Z., Xu M, & Han T. (2023). Activation of melanocortin-1 receptor signaling in melanoma cells impairs T cell infiltration to dampen antitumor immunity. Nature Communications, 14, 5740.

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Histological Analysis of Liver and Spleen

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Livers and spleen sections were fixed in 10% neutral buffered formalin (NBF), underwent paraffin-embedded sectioning (2 µm) and stained with Hematoxylin & Eosin (H&E) and Periodic acid-Schiff (PAS). Histological images were generated from VS120 Virtual Slide Microscope (Olympus) and OlyVIA software.

Kandalgaonkar M.R., Yeoh B.S., Joe B., Schmidt N.W., Vijay-Kumar M, & Saha P. (2024). Hypertension Increases Susceptibility to Experimental Malaria in Mice. Function, 5(3), zqae009.

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