N sim analysis software

Manufactured by Nikon

N-SIM analysis software is a tool designed for image processing and analysis of data generated by Nikon's N-SIM super-resolution microscopy system. It provides functionality for visualizing, processing, and analyzing high-resolution images without interpreting or extrapolating the intended use of the product.

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Lab products found in correlation

Confocal microscopy system, by Nikon (2 mentions) Vw h2ma, by Keyence (2 mentions) Bz x700 all in one fluorescence microscope, by Keyence (2 mentions) Bz x analyzer, by Keyence (2 mentions) Incubation system s, by Zeiss (1 mentions) Zen 2012, by Zeiss (1 mentions)

3 protocols using n sim analysis software

Visualizing Mitochondrial Dynamics in Leigh Syndrome

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For live-cell imaging microscopy, culture dishes with fibroblasts from Leigh syndrome patient following Mitotracker (green) staining were placed into a LSM780 Zeiss confocal microscopy system equipped with incubation system S (Carl Zeiss). ZEN2012 software (Carl Zeiss) was used to analyze the trajectory of each mitochondrion.
For super resolution images, cells from a Leigh syndrome patient were stained with MitoRed (shown in red) and the nucleus counterstained with Hoechst3342 (shown in blue). The samples were then placed into a Nikon N-SIM super resolution microscopy system (Nikon). Images were acquired and the data analyzed using NIS-Elements with N-SIM analysis software (Nikon). Electron microscopic analysis was performed as previously reported (Ogata et al., 2015 (link)).

Matsuhashi T., Sato T., Kanno S.I., Suzuki T., Matsuo A., Oba Y., Kikusato M., Ogasawara E., Kudo T., Suzuki K., Ohara O., Shimbo H., Nanto F., Yamaguchi H., Saigusa D., Mukaiyama Y., Watabe A., Kikuchi K., Shima H., Mishima E., Akiyama Y., Oikawa Y., Hsin-Jung H., Akiyama Y., Suzuki C., Uematsu M., Ogata M., Kumagai N., Toyomizu M., Hozawa A., Mano N., Owada Y., Aiba S., Yanagisawa T., Tomioka Y., Kure S., Ito S., Nakada K., Hayashi K.I., Osaka H, & Abe T. (2017). Mitochonic Acid 5 (MA-5) Facilitates ATP Synthase Oligomerization and Cell Survival in Various Mitochondrial Diseases. EBioMedicine, 20, 27-38.

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Imaging and Analyzing Mitochondria in sIBM Cells

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To obtain images of mitochondria, cells from sIBM patients were stained with MitoTracker red (a molecular probe, shown in red), and the nuclei were counterstained with 4',6-diamidino-2-phenylindole (DAPI, shown in blue). The samples were then placed into a confocal microscopy system (Nikon, Tokyo, Japan). Images were acquired and analyzed using NIS-Elements with N-SIM analysis software (Nikon) and ImageJ. Briefly, the MitoTracker red signal in the images was changed to grayscale, and a suitable threshold level that allowed the signal intensity of the mitochondria to be distinguished from the background noise was set in ImageJ software. The lengths of the major and minor axes of the mitochondria were measured using ImageJ. Electron microscopy analysis was performed as previously reported [12 (link), 16 (link)]. For live-cell imaging, culture dishes with myoblasts and fibroblasts from sIBM patients stained with MitoTracker Green were placed into a KEYENCE BZ-X700 All-in-one Fluorescence Microscope (KEYENCE, Osaka, Japan). Images were taken for 5 min and converted to movie files using a BZ-X Analyzer (KEYENCE). The movies were analyzed with the video editing analysis software VW-H2MA (KEYENCE) to evaluate cell migration [17 (link)].

Oikawa Y., Izumi R., Koide M., Hagiwara Y., Kanzaki M., Suzuki N., Kikuchi K., Matsuhashi T., Akiyama Y., Ichijo M., Watanabe S., Toyohara T., Suzuki T., Mishima E., Akiyama Y., Ogata Y., Suzuki C., Hayashi H., Kodama E.N., Hayashi K.I., Itoi E., Aoki M., Kure S, & Abe T. (2020). Mitochondrial dysfunction underlying sporadic inclusion body myositis is ameliorated by the mitochondrial homing drug MA-5. PLoS ONE, 15(12), e0231064.

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Mitochondrial Imaging in sIBM Cells

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To obtain images of mitochondria, cells from sIBM patients were stained with MitoTracker red (a molecular probe, shown in red), and the nuclei were counterstained with 4',6-diamidino-2-phenylindole (DAPI, shown in blue). The samples were then placed into a confocal microscopy system (Nikon, Tokyo, Japan). Images were acquired and analyzed using NIS-Elements with N-SIM analysis software (Nikon) and ImageJ.
Briefly, the MitoTracker red signal in the images was changed to grayscale, and a suitable threshold level that allowed the signal intensity of the mitochondria to be distinguished from the background noise was set in ImageJ software. The lengths of the major and minor axes of the mitochondria were measured using ImageJ. Electron microscopy analysis was performed as previously reported [12, 16] . For live-cell imaging, culture dishes with myoblasts and fibroblasts from sIBM patients stained with MitoTracker Green were placed into a KEYENCE BZ-X700 All-in-one Fluorescence Microscope (KEYENCE, Osaka, Japan). Images were taken for 5 min and converted to movie files using a BZ-X Analyzer (KEYENCE). The movies were analyzed with the video editing analysis software VW-H2MA (KEYENCE) to evaluate cell migration [17] .

Oikawa Y., Izumi R., Koide M., Hagiwara Y., Kanzaki M., Suzuki N., Kikuchi K., Matsuhashi T., Akiyama Y., Ichijo M., Toyohara T., Suzuki T., Mishima E., Akiyama Y., Ogata Y., Suzuki C., Aoki M., Itoi E., Kure S., Hayashi K., & Abe T. (2020). Mitochondrial dysfunction underlying sporadic inclusion body myositis is ameliorated by the mitochondrial homing drug MA-5.

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