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N storm software

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N-STORM software is a high-resolution imaging system developed by Nikon. It is designed to enable super-resolution microscopy techniques, allowing users to capture images with resolutions beyond the diffraction limit of light. The software provides the necessary tools and algorithms to process and analyze super-resolution data obtained from compatible Nikon microscope systems.

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Lab products found in correlation

N storm microscope, by Nikon (3 mentions) Alexa fluor 647 phalloidin, by Thermo Fisher Scientific (2 mentions)

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N-STORM (43 citations)

4 protocols using n storm software

1

Super-Resolution Microscopy Image Processing

Cited 4 times
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For Fig. 4 images were reconstructed using NanoJ-SRRF12 (link) (magnification: 4, temporal analysis settings: TRPPM for live-cell data and TRM for fixed-cell data). Drift was estimated using the inbuilt function in NanoJ-SRRF and correction applied during SRRF analysis. For Fig. 5 localisations were detected using the N-STORM software (Nikon), and exported as a text file before being filtered (number of photons between 700 and 50,000; number of detections (after linking across frames) <50 frames) and rendered using ThunderSTORM33 (link). Additionally, a 32 nm radius Gaussian blur (ImageJ/Gaussian blur) and a Gamma correction (ImageJ/Gamma, varying between 0.6 and 1.5) were applied. Chromatic aberration between the red (561 nm) and far-red (647 nm) channels were corrected within the N-STORM software using polynomial warping and remaining translational drift between acquisition passes were aligned manually on high-resolution reconstructions.
The image resolution was estimated by calculating the Fourier Ring Correlation (FRC)34 (link) with the typical 1/7 threshold using NanoJ-SQUIRREL plugin and reconstructing the original dataset separated into two different stacks composed of odd or even images15 (link). NanoJ-SRRF, NanoJ-SQUIRREL and ThunderSTORM are available in Fiji20 (link).
Almada P., Pereira P.M., Culley S., Caillol G., Boroni-Rueda F., Dix C.L., Charras G., Baum B., Laine R.F., Leterrier C, & Henriques R. (2019). Automating multimodal microscopy with NanoJ-Fluidics. Nature Communications, 10, 1223.
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2

Super-Resolution Imaging of Actin and Myosin in Neurons

Cited 1 time
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STORM imaging was performed on an N-STORM microscope (Nikon) as previously described (Leterrier et al, 2015 (link)). After locating a suitable neuron using low-intensity illumination, an epifluorescence image was acquired followed by STORM acquisition. Alexa 647-conjugated pMLC was imaged first in STORM buffer (Abbelight) using 647 nm laser excitation, recording 50,000 frames at 67 Hz. Medium was then exchanged with a phosphate buffer (pH 7.4, 0.1 M) for imaging the Atto 488-conjugated phalloidin using 488 nm laser excitation, recording 50,000 frames at 67 Hz. N-STORM software (Nikon) was used for localization of single fluorophore activations and the correction of chromatic aberration and shift between channels. The list of localizations was then exported as a text file. Image reconstructions were performed using the ThunderSTORM ImageJ plugin (Ovesny et al., 2014 (link)) in Fiji software. Custom scripts and macros were used to translate localization files from N-STORM to ThunderSTORM formats, as well as to automate image reconstruction for whole images, detailed zooms, and YZ transverse projections (Leterrier et al, 2015 (link)). Actin images were equally adjusted with a global 0.7 gamma factor to aid visualization of faint structures.
Berger S.L., Leo-Macias A., Yuen S., Khatri L., Pfennig S., Zhang Y., Agullo-Pascual E., Caillol G., Zhu M., Rothenberg E., Melendez-Vasquez C.V., Delmar M., Leterrier C, & Salzer J.L. (2018). Localized myosin II activity regulates assembly and plasticity of the axon initial segment. Neuron, 97(3), 555-570.e6.
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3

Super-Resolution Imaging of Actin Filaments

Cited 2 times
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After fixation and immunolabeling 55 (link), cells were incubated with phalloidin-Alexa-Fluor-647 (0.5 µM, Thermo Fisher) overnight at 4°C. After two quick rinses in phosphate buffer, RPE1 cells were mounted in a closed chamber in STORM buffer (Smart kit, Abbelight) and imaged by STORM as described previously 57 (link) using an N-STORM microscope (Nikon Instruments) equipped with an Ixon DU-897 camera (Andor) and controled with Nikon Elements. Phalloidin (0.25µM) was added in the STORM medium to mitigate progressive unbinding from actin filaments during imaging 55 (link). After locating a cell using low-intensity illumination, epifluorescence images were acquired in both the green and far-red channels. For STORM imaging of actin, the sample was continuously illuminated at 647nm (full power) and a series of 60000 to 100000 images (256x256 pixels, 15 ms exposure time). The N-STORM software (Nikon Instruments) was used for the localization of single fluorophore activations. After filtering, localizations with more than 800 photons, the list of localizations was exported as a text file and the ThunderSTORM plugin 58 (link) of Fiji was used to generate reconstructions.
Vignaud T., Copos C., Leterrier C., Toro-Nahuelpan M., Tseng Q., Mahamid J., Blanchoin L., Mogilner A., Théry M, & Kurzawa L. (2020). Stress fibers are embedded in a contractile cortical network. Nature materials, 20(3), 410-420.
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4

Super-Resolution Imaging of Actin Filaments

Cited 2 times
Check if the same lab product or an alternative is used in the 5 most similar protocols
After fixation and immunolabeling 55 (link), cells were incubated with phalloidin-Alexa-Fluor-647 (0.5 µM, Thermo Fisher) overnight at 4°C. After two quick rinses in phosphate buffer, RPE1 cells were mounted in a closed chamber in STORM buffer (Smart kit, Abbelight) and imaged by STORM as described previously 57 (link) using an N-STORM microscope (Nikon Instruments) equipped with an Ixon DU-897 camera (Andor) and controled with Nikon Elements. Phalloidin (0.25µM) was added in the STORM medium to mitigate progressive unbinding from actin filaments during imaging 55 (link). After locating a cell using low-intensity illumination, epifluorescence images were acquired in both the green and far-red channels. For STORM imaging of actin, the sample was continuously illuminated at 647nm (full power) and a series of 60000 to 100000 images (256x256 pixels, 15 ms exposure time). The N-STORM software (Nikon Instruments) was used for the localization of single fluorophore activations. After filtering, localizations with more than 800 photons, the list of localizations was exported as a text file and the ThunderSTORM plugin 58 (link) of Fiji was used to generate reconstructions.
Vignaud T., Copos C., Leterrier C., Toro-Nahuelpan M., Tseng Q., Mahamid J., Blanchoin L., Mogilner A., Théry M, & Kurzawa L. (2020). Stress fibers are embedded in a contractile cortical network. Nature materials, 20(3), 410-420.
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