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Fiji imagej

Manufactured by LI COR
Sourced in United States

Fiji ImageJ is an open-source image processing software designed for scientific imaging. It provides a comprehensive set of tools for image analysis, processing, and visualization. The software's core function is to facilitate the management, manipulation, and interpretation of digital images from various sources, including microscopes, cameras, and scanners.

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4 protocols using fiji imagej

1

Quantifying Fluorescent Signals and Immunoblot Analysis

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Fluorescent signals were quantified with Fiji ImageJ (http://fiji.sc/wiki/index.php/Fiji) or the Volocity 3D Image Analysis software (Improvision). Immunoblots were analyzed by Fiji ImageJ or Image Studio (Licor Bioscience, Lincoln, NE, USA). Graphical presentations were made using Graph Pad Prism (Graph Pad Software, La Jolla, CA, USA).
Statistical analyses were performed by Graph Pad Prism using Student's t test for independent samples or one-way Anova.
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2

Multimodal Experimental Techniques for Biomolecular Analysis

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Flow cytometry: FlowJo ver. 10 (Beckton Dickinson). Western blots: Image Studio ver. 5 (Li-Cor) and Fiji ImageJ ver. 1.52p [45 (link)]. Confocal microscopy: NIS Elements software ver. 5.20.01 (Nikon). Statistical analysis: Prism ver. 8 (GraphPad). Protein structure rendering: Open-source PyMOL ver. 1.8 [46 ]. Figure assembly and illustration: CorelDRAW ver. 2019 (Corel).
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3

Quantification of alpha-synuclein in mouse brain

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Brains from male and female mice 3–4 months of age were dissected immediately postmortem, and olfactory bulbs and cerebellum were removed. Remaining brain tissue was prepared for western blot analysis via use of Syn-PER Synaptic Protein Extraction Reagent (Thermo Fisher) using the manufacturer’s protocol, resulting in both a synaptosomal and a cytosolic fraction. Samples were run on a 4–12% Tris-glycine gels (Invitrogen) for 2 h and 45 min at 80 V. Gels were transferred onto Immobilon-FL membranes (0.45 μm pore; Millipore) at 25 V for 18 h at 4 °C. Membranes were blocked with Odyssey blocking buffer (Li-COR Biosciences) for 1 h at room temperature. Membranes were incubated overnight with primary antibodies (alpha-synuclein: 1:1000, Syn-1, BD Biosciences; serine-129 phospho-alpha-synuclein: 1:1000, EP1536Y, Abcam; GAPDH: GAPDH, 1:10,000, Millipore). A near infrared fluorescent-labeled secondary antibodies (1:5000; IR800 & IR700; LI-COR Biosciences) were used, and quantification was done with an Odyssey CLx infrared imaging system (LI-COR Biosciences) and ImageJ/Fiji (NIH).
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4

Quantitative Analysis of Alpha-Synuclein Levels

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Brains from male WT SynGFP [61 (link)], E46K SynGFP and A53T SynGFP that were 3–4 months of age were dissected immediately post mortem and olfactory bulbs and cerebellum removed. Remaining brain tissue was homogenized in ice-cold lysis buffer (50 mm Tris–HCl, pH 7.5, 5 M guanidinium, protease inhibitor mixture (Roche Complete)) using a probe-tip sonicator, then centrifuged (13,000 × g, 10 min) and supernatant was stored at −80 °C until analysis. On the day of analysis total protein concentration was determined using a BCA assay. Total cell lysates (12 μg of protein) were solubilized in LDS (lithium dodecyl sulfate) buffer under reducing conditions. Proteins were separated by SDS-PAGE using a 12% Bis–Tris gel and transferred to a PVDF membrane. Following blocking with blocking buffer (LI-COR Biosciences), membranes were incubated overnight with primary antibodies (alpha-synuclein: 1:1000, Syn-1, BD Biosciences; GAPDH: GAPDH, 1:10,000, Millipore). A near infrared fluorescent-labeled secondary antibody (1:5000; IR800CW; LI-COR Biosciences) was used and quantification was done with an Odyssey CLx infrared imaging system (LI-COR Biosciences) and ImageJ/Fiji (NIH).
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