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deconvolution software  (Nikon)


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    Structured Review

    Nikon deconvolution software
    Fig. 1 | Implementation and benchmarking of Deconwolf. a, Schematic Deconwolf workflow. WSI, whole-slide image. b,c, In silico generated microtubule images before (ground truth) (b) and after adding artificial noise to simulate a real image (c). Maximum z-projection is shown. d, MSE after deconvolving the image in c using the default Deconwolf mode with scaled heavy ball15 acceleration (DW_SHB), or Deconwolf based on the classic Richardson–Lucy <t>deconvolution</t> method (DW_RL)2,3. The dashed vertical lines indicate the number of iterations needed to reach the minimum MSE. e, As in c after deconvolution with Deconwolf (DW) using default settings. it, number of iterations. t, deconvolution time measured on an 8-Core AMD Ryzen 7 3700X machine. f, As in c using DeconvolutionLab2 (DL2) with default settings at 115 iterations. g, As in
    Deconvolution Software, supplied by Nikon, used in various techniques. Bioz Stars score: 99/100, based on 40098 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/nis+elements+deconvolution+software/NIS-Elements/pm38844629-174-32-34
    Average 99 stars, based on 40098 article reviews
    deconvolution software - by Bioz Stars, 2026-11
    99/100 stars

    Images

    1) Product Images from "Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images."

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.

    Journal: Nature methods

    doi: 10.1038/s41592-024-02294-7

    Fig. 1 | Implementation and benchmarking of Deconwolf. a, Schematic Deconwolf workflow. WSI, whole-slide image. b,c, In silico generated microtubule images before (ground truth) (b) and after adding artificial noise to simulate a real image (c). Maximum z-projection is shown. d, MSE after deconvolving the image in c using the default Deconwolf mode with scaled heavy ball15 acceleration (DW_SHB), or Deconwolf based on the classic Richardson–Lucy deconvolution method (DW_RL)2,3. The dashed vertical lines indicate the number of iterations needed to reach the minimum MSE. e, As in c after deconvolution with Deconwolf (DW) using default settings. it, number of iterations. t, deconvolution time measured on an 8-Core AMD Ryzen 7 3700X machine. f, As in c using DeconvolutionLab2 (DL2) with default settings at 115 iterations. g, As in
    Figure Legend Snippet: Fig. 1 | Implementation and benchmarking of Deconwolf. a, Schematic Deconwolf workflow. WSI, whole-slide image. b,c, In silico generated microtubule images before (ground truth) (b) and after adding artificial noise to simulate a real image (c). Maximum z-projection is shown. d, MSE after deconvolving the image in c using the default Deconwolf mode with scaled heavy ball15 acceleration (DW_SHB), or Deconwolf based on the classic Richardson–Lucy deconvolution method (DW_RL)2,3. The dashed vertical lines indicate the number of iterations needed to reach the minimum MSE. e, As in c after deconvolution with Deconwolf (DW) using default settings. it, number of iterations. t, deconvolution time measured on an 8-Core AMD Ryzen 7 3700X machine. f, As in c using DeconvolutionLab2 (DL2) with default settings at 115 iterations. g, As in

    Techniques Used: In Silico, Generated

    Fig. 5 | Deconwolf enables robust detection of individual transcripts in low-magnification smFISH images. a, Breast adenocarcinoma tissue section stained with an smFISH probe targeting MKI67 transcripts (white) and imaged on a widefield microscope using a ×20 air objective, after deconvolution with Deconwolf (DW). Maximum z-projection is shown. Blue, DNA. Scale bars, 200 μm in the large left panel; 10 μm in the two small panels on the right. b,c, Zoom-in of the regions (R1 and R2) marked by the white dashed squares in a. Scale bars, 10 μm. d, Left plot: probability density function (PDF) of smFISH dot fluorescence
    Figure Legend Snippet: Fig. 5 | Deconwolf enables robust detection of individual transcripts in low-magnification smFISH images. a, Breast adenocarcinoma tissue section stained with an smFISH probe targeting MKI67 transcripts (white) and imaged on a widefield microscope using a ×20 air objective, after deconvolution with Deconwolf (DW). Maximum z-projection is shown. Blue, DNA. Scale bars, 200 μm in the large left panel; 10 μm in the two small panels on the right. b,c, Zoom-in of the regions (R1 and R2) marked by the white dashed squares in a. Scale bars, 10 μm. d, Left plot: probability density function (PDF) of smFISH dot fluorescence

    Techniques Used: Staining, Microscopy, Fluorescence

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    Article Title: Sirt3 deficiency impairs AMPK-Acc1 antilipogenic signaling in female adipocytes.
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    Microscopy:

    Article Title: Mechanisms of Hexavalent Chromium-Induced Lung Carcinogenesis: DNA Double-Strand Breaks and DNA Repair Inhibition in a Guinea Pig Model.
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    Article Title: Sirt3 deficiency impairs AMPK-Acc1 antilipogenic signaling in female adipocytes.
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    Article Title: Trichoderma harzianum M2 Induces Systemic Resistance to Fusarium Crown Rot and Remodels Root Architecture to Promote Phosphorus Uptake in Wheat.
    Article Snippet: .. Putative positive transformants were further verified by PCR amplification of the GFP gene, and GFP fluorescence signal was detected using a Nikon confocal microscope (AX NIS-Elements 5.4, Tokyo, Japan) to confirm GFP expression. ..

    Software:

    Article Title: Mechanisms of Hexavalent Chromium-Induced Lung Carcinogenesis: DNA Double-Strand Breaks and DNA Repair Inhibition in a Guinea Pig Model.
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    Article Title: Peripheral nerve injury alters metabolic function and neuronal excitability through the Lin28/let-7 pathway
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    Article Title: Prenatal microplastic exposure-induced testicular developmental toxicity and its long-term hazards in male rat offspring.
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    Article Title: Sirt3 deficiency impairs AMPK-Acc1 antilipogenic signaling in female adipocytes.
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    Fluorescence:

    Article Title: Peripheral nerve injury alters metabolic function and neuronal excitability through the Lin28/let-7 pathway
    Article Snippet: .. Image pairs were continually acquired at 340-nm 100-ms excitation and 380-nm 200-ms excitation at 1.5-s intervals using an inverted fluorescence microscope (TE200, Nikon) equipped with a complementary metal-oxide semiconductor camera (Neo, Andor) and an automated filter wheel (Lambda), controlled by the NIS elements software (Nikon), and emission at 340/380 nm was calculated. .. Cells were imaged during continuous perfusion with CIB and then challenged with sequential 30-s applications of 15 mM KCl, capsaicin (10 nM; Sigma-Aldrich), and 50 mM KCl, with 3-min intervening washouts with CIB.

    Article Title: Prenatal microplastic exposure-induced testicular developmental toxicity and its long-term hazards in male rat offspring.
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    Article Title: Trichoderma harzianum M2 Induces Systemic Resistance to Fusarium Crown Rot and Remodels Root Architecture to Promote Phosphorus Uptake in Wheat.
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    Article Title: Expanded characterization of the valproic acid zebrafish larval model of autism spectrum disorder: Insights into dysregulation in the gut
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    Automated:

    Article Title: Peripheral nerve injury alters metabolic function and neuronal excitability through the Lin28/let-7 pathway
    Article Snippet: .. Image pairs were continually acquired at 340-nm 100-ms excitation and 380-nm 200-ms excitation at 1.5-s intervals using an inverted fluorescence microscope (TE200, Nikon) equipped with a complementary metal-oxide semiconductor camera (Neo, Andor) and an automated filter wheel (Lambda), controlled by the NIS elements software (Nikon), and emission at 340/380 nm was calculated. .. Cells were imaged during continuous perfusion with CIB and then challenged with sequential 30-s applications of 15 mM KCl, capsaicin (10 nM; Sigma-Aldrich), and 50 mM KCl, with 3-min intervening washouts with CIB.

    Imaging:

    Article Title: Sirt3 deficiency impairs AMPK-Acc1 antilipogenic signaling in female adipocytes.
    Article Snippet: 1 Division of Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia 2 Division of Materials Chemistry, Rudjer Boskovic Institute, Zagreb, Croatia 3 Faculty of Science, Department of Biology, University of Zagreb, Zagreb, Croatia 4 Faculty of Biology, Center for Electron Microscopy, University of Belgrade, Belgrade, Serbia Abstract Background Background: Biological sex influences adipose tissue function, while impaired adipogenesis contributes to adipose dysfunction.. Sirtuin 3 (Sirt3), a mitochondrial NAD+-dependent deacetylase involved in oxidative metabolism and stress adaptation, remains insufficiently defined in adipogenic differentiation.. We investigated how Sirt3 and sex shape adipogenic phenotype in mouse embryonic fibroblast (MEF)-derived adipocytes.

    Inverted Microscopy:

    Article Title: Sirt3 deficiency impairs AMPK-Acc1 antilipogenic signaling in female adipocytes.
    Article Snippet: 1 Division of Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia 2 Division of Materials Chemistry, Rudjer Boskovic Institute, Zagreb, Croatia 3 Faculty of Science, Department of Biology, University of Zagreb, Zagreb, Croatia 4 Faculty of Biology, Center for Electron Microscopy, University of Belgrade, Belgrade, Serbia Abstract Background Background: Biological sex influences adipose tissue function, while impaired adipogenesis contributes to adipose dysfunction.. Sirtuin 3 (Sirt3), a mitochondrial NAD+-dependent deacetylase involved in oxidative metabolism and stress adaptation, remains insufficiently defined in adipogenic differentiation.. We investigated how Sirt3 and sex shape adipogenic phenotype in mouse embryonic fibroblast (MEF)-derived adipocytes.

    Article Title: Expanded characterization of the valproic acid zebrafish larval model of autism spectrum disorder: Insights into dysregulation in the gut
    Article Snippet: Magnesium sulfate (208094, Sigma‐Aldrich, Wisconsin, United States; 33.2 mmol/L) and atropine (A0257, Sigma‐Aldrich, St Louis, United States; 5 mmol/L) were included as positive controls to mimic accelerated and delayed gut motility, respectively. .. Larvae were anesthetized and orientated as described in the NR protocol before live images of gut fluorescence were acquired at 100× magnification (Nikon ECLIPSE Ti2 inverted microscope, NiS‐Elements D, version 5.30.02 software). .. Brightfield images of the gut were overlaid with fluorescent images to accurately demarcate the region of interest before quantification of gut fluorescent intensity (using ImageJ software).

    Analysis:

    Article Title: Sirt3 deficiency impairs AMPK-Acc1 antilipogenic signaling in female adipocytes.
    Article Snippet: 1 Division of Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia 2 Division of Materials Chemistry, Rudjer Boskovic Institute, Zagreb, Croatia 3 Faculty of Science, Department of Biology, University of Zagreb, Zagreb, Croatia 4 Faculty of Biology, Center for Electron Microscopy, University of Belgrade, Belgrade, Serbia Abstract Background Background: Biological sex influences adipose tissue function, while impaired adipogenesis contributes to adipose dysfunction.. Sirtuin 3 (Sirt3), a mitochondrial NAD+-dependent deacetylase involved in oxidative metabolism and stress adaptation, remains insufficiently defined in adipogenic differentiation.. We investigated how Sirt3 and sex shape adipogenic phenotype in mouse embryonic fibroblast (MEF)-derived adipocytes.

    Light Microscopy:

    Article Title: Leptin promotes obesity‑related osteoarthritis progression via CD44/JAK2/STAT3 axis‑mediated chondrocyte apoptosis.
    Article Snippet: .. Following dehydration in increasing ethanol concentrations (70‐100%) and xylene clearing, the slides were mounted with neutral balsam and images were captured under a Nikon Eclipse 80i light microscope (Nikon Corporation,) using NIS‐Elements BR software (version 5.42; Nikon Corporation). ..

    Polymerase Chain Reaction:

    Article Title: Trichoderma harzianum M2 Induces Systemic Resistance to Fusarium Crown Rot and Remodels Root Architecture to Promote Phosphorus Uptake in Wheat.
    Article Snippet: .. Putative positive transformants were further verified by PCR amplification of the GFP gene, and GFP fluorescence signal was detected using a Nikon confocal microscope (AX NIS-Elements 5.4, Tokyo, Japan) to confirm GFP expression. ..

    Amplification:

    Article Title: Trichoderma harzianum M2 Induces Systemic Resistance to Fusarium Crown Rot and Remodels Root Architecture to Promote Phosphorus Uptake in Wheat.
    Article Snippet: .. Putative positive transformants were further verified by PCR amplification of the GFP gene, and GFP fluorescence signal was detected using a Nikon confocal microscope (AX NIS-Elements 5.4, Tokyo, Japan) to confirm GFP expression. ..

    Expressing:

    Article Title: Trichoderma harzianum M2 Induces Systemic Resistance to Fusarium Crown Rot and Remodels Root Architecture to Promote Phosphorus Uptake in Wheat.
    Article Snippet: .. Putative positive transformants were further verified by PCR amplification of the GFP gene, and GFP fluorescence signal was detected using a Nikon confocal microscope (AX NIS-Elements 5.4, Tokyo, Japan) to confirm GFP expression. ..



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    Image Search Results


    Fig. 1 | Implementation and benchmarking of Deconwolf. a, Schematic Deconwolf workflow. WSI, whole-slide image. b,c, In silico generated microtubule images before (ground truth) (b) and after adding artificial noise to simulate a real image (c). Maximum z-projection is shown. d, MSE after deconvolving the image in c using the default Deconwolf mode with scaled heavy ball15 acceleration (DW_SHB), or Deconwolf based on the classic Richardson–Lucy deconvolution method (DW_RL)2,3. The dashed vertical lines indicate the number of iterations needed to reach the minimum MSE. e, As in c after deconvolution with Deconwolf (DW) using default settings. it, number of iterations. t, deconvolution time measured on an 8-Core AMD Ryzen 7 3700X machine. f, As in c using DeconvolutionLab2 (DL2) with default settings at 115 iterations. g, As in

    Journal: Nature methods

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.

    doi: 10.1038/s41592-024-02294-7

    Figure Lengend Snippet: Fig. 1 | Implementation and benchmarking of Deconwolf. a, Schematic Deconwolf workflow. WSI, whole-slide image. b,c, In silico generated microtubule images before (ground truth) (b) and after adding artificial noise to simulate a real image (c). Maximum z-projection is shown. d, MSE after deconvolving the image in c using the default Deconwolf mode with scaled heavy ball15 acceleration (DW_SHB), or Deconwolf based on the classic Richardson–Lucy deconvolution method (DW_RL)2,3. The dashed vertical lines indicate the number of iterations needed to reach the minimum MSE. e, As in c after deconvolution with Deconwolf (DW) using default settings. it, number of iterations. t, deconvolution time measured on an 8-Core AMD Ryzen 7 3700X machine. f, As in c using DeconvolutionLab2 (DL2) with default settings at 115 iterations. g, As in

    Article Snippet: Visual inspection of the images in the original dataset showed densely packed clouds of fluorescent dots in different colors inside each nucleus, which could be only partially resolved by applying the commercial deconvolution software (Nikon NIS Elements AR, v5.02.0) incorporated in the OligoFISSEQ image processing pipeline (Fig. 6c).

    Techniques: In Silico, Generated

    Fig. 5 | Deconwolf enables robust detection of individual transcripts in low-magnification smFISH images. a, Breast adenocarcinoma tissue section stained with an smFISH probe targeting MKI67 transcripts (white) and imaged on a widefield microscope using a ×20 air objective, after deconvolution with Deconwolf (DW). Maximum z-projection is shown. Blue, DNA. Scale bars, 200 μm in the large left panel; 10 μm in the two small panels on the right. b,c, Zoom-in of the regions (R1 and R2) marked by the white dashed squares in a. Scale bars, 10 μm. d, Left plot: probability density function (PDF) of smFISH dot fluorescence

    Journal: Nature methods

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.

    doi: 10.1038/s41592-024-02294-7

    Figure Lengend Snippet: Fig. 5 | Deconwolf enables robust detection of individual transcripts in low-magnification smFISH images. a, Breast adenocarcinoma tissue section stained with an smFISH probe targeting MKI67 transcripts (white) and imaged on a widefield microscope using a ×20 air objective, after deconvolution with Deconwolf (DW). Maximum z-projection is shown. Blue, DNA. Scale bars, 200 μm in the large left panel; 10 μm in the two small panels on the right. b,c, Zoom-in of the regions (R1 and R2) marked by the white dashed squares in a. Scale bars, 10 μm. d, Left plot: probability density function (PDF) of smFISH dot fluorescence

    Article Snippet: Visual inspection of the images in the original dataset showed densely packed clouds of fluorescent dots in different colors inside each nucleus, which could be only partially resolved by applying the commercial deconvolution software (Nikon NIS Elements AR, v5.02.0) incorporated in the OligoFISSEQ image processing pipeline (Fig. 6c).

    Techniques: Staining, Microscopy, Fluorescence