Formalin-fixed mouse half-brains were cut into four sections prior to processing through graded alcohols, clearing with xylene, infiltrating with paraffin, and embedding. Thin sections (8 μm) were cut, collected on slides, deparaffinized, and exposed to heat-mediated antigen retrieval with citrate buffer (0.1 M; pH 6) for 20 min. Slides were stained using the Thermo Fisher 480S Autostainer with 30 min blocking in 10% (vol/vol) normal goat serum and incubating with primary and secondary antibodies (2 h each). Primary antibody binding of phosphorylated (S129) α-synuclein (EP1536Y; 1:1,000; Abcam) and glial fibrillary acidic protein (GFAP; 1:500; Abcam) were detected using secondary antibodies conjugated to AlexaFluor 488 or 647 (1:500; Thermo Fisher Scientific). Slides were imaged using the Zeiss AxioScan. Z1 and were then analyzed using the ZEN Analysis software package (Zeiss). To quantify α-synuclein neuropathology, a pixel intensity threshold was determined using a positive control slide. Regions of interest were drawn around the caudoputamen (Cd), hippocampus (HC), piriform cortex and amygdala (PC), thalamus (Thal), hypothalamus (HTH), midbrain (Mid), and pons. The percentage of positively stained pixels in each region was determined and averaged across inoculation groups.
Zen analysis software package
Manufactured by Zeiss
The ZEN Analysis software package is a comprehensive imaging and analysis solution developed by Zeiss. It provides a suite of tools for the acquisition, processing, and analysis of microscopy data. The software supports a wide range of imaging modalities and enables users to perform advanced image analysis tasks.
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Lab products found in correlation
3 protocols using zen analysis software package
1
Quantifying α-Synuclein Neuropathology in Mice
2
Quantifying α-Synuclein Pathology in Mouse Brain
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Formalin-fixed mouse half-brains were cut into four sections prior to processing through graded alcohols, clearing with xylene, infiltrating with paraffin, and embedding. Thin sections (8 μm) were cut, collected on slides, deparaffinized, and exposed to heat-mediated antigen retrieval with citrate buffer (0.1 M, pH 6) for 20 min. Slides were stained using the Thermo Fisher 480S Autostainer with 30 min blocking in 10% (vol/vol) normal goat serum and incubating with primary and secondary antibodies (2 h each). Primary antibodies used include phosphorylated (S129) α-synuclein (EP1536Y; 1:1,000; Abcam) and glial fibrillary acidic protein (GFAP; 1:500; Abcam). Secondary antibodies conjugated to AlexaFluor 488 or 647 (1:500; Thermo Fisher) were used. Slides were imaged using the Zeiss AxioScan.Z1 and were then analyzed using the ZEN Analysis software package (Zeiss). To quantify α-synuclein neuropathology, a pixel intensity threshold was determined using a positive control slide. Regions of interest were drawn around the caudoputamen, hippocampus, piriform cortex and amygdala, thalamus, hypothalamus, midbrain, and pons. The percentage of pixels positive for staining in each region was determined and averaged across inoculation groups.
3
Quantifying Synuclein Neuropathology in Mouse Brains
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Mouse brains were fixed in 10% (vol/vol) formalin, processed, embedded, and sectioned as previously described [25 (link)]. Brains were cut into four sections prior to processing through graded alcohols, clearing with xylene, infiltrating with paraffin, and embedding. After deparaffinization, sections were exposed to heat-mediated antigen retrieval with citrate buffer (0.1 M, pH 6) for 20 min. Slides were stained overnight at room temperature after blocking in 10% (vol/vol) normal goat serum using EP1536Y (pS129 α-synuclein; 1:1,000; Abcam), p62 (Anti-SQSTM1; 1:1,000; Abcam), and glial fibrillary acidic protein (GFAP; 1:500; Abcam) primary antibodies. Secondary antibodies conjugated to AlexaFluor 488, 568, or 647 (Thermo Fisher) were used to detect immunolabeling.
Slides were imaged using the Zeiss AxioScan.Z1. Digital images were analyzed using the Zen Analysis software package (Zeiss). To quantify α-synuclein neuropathology, a pixel intensity threshold was determined using a positive control slide and was then applied to all slides. Regions of interest were drawn around the HC, Thal, HTH, midbrain (Mid), and pons. The percentage of pixels positive for staining in each region was determined.
Slides were imaged using the Zeiss AxioScan.Z1. Digital images were analyzed using the Zen Analysis software package (Zeiss). To quantify α-synuclein neuropathology, a pixel intensity threshold was determined using a positive control slide and was then applied to all slides. Regions of interest were drawn around the HC, Thal, HTH, midbrain (Mid), and pons. The percentage of pixels positive for staining in each region was determined.
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