Pipeline for Image Processing and Quantification of Striatal Dopamine Innervation using Fiji (IF/IHC)
By onThis protocol outlines the image preprocessing steps required prior to analysis with ImageJ tools as well as the ImageJ pipeline to quantify striatal innervation.
Analyses of mitochondrial function in SNpc with the Seahorse XFe96
By onProtocol for analyses of mitochondrial function in SNpc with the Seahorse XFe96
Tissue Mito-IP: Immunopurification of Mitochondria from MitoTag Mice
By onA novel method called 'Mito-IP' enables rapid immunopurification of pure mitochondria in 10 minutes using a chimeric protein with HA tags, improving organelle isolation for various analyses.
Immunostaining Mouse Tissue
By onProtocol used in the Gradinaru lab for immunohistochemistry to analyze protein expression in the mouse brain
Western Blot with iBind System
By onProtocol used in the Gradinaru lab for western blot using the iBind Automated Western System
Open Field & Cylinder test Behavior Assays
By onProtocols for mouse behavioral studies using the open field test and the cylinder test from Fushiki et al 2024.
Non-human Primate Arm-reaching Behavioral Tasks
By onProtocol for training and testing non-human primates in arm-reaching tasks to evaluate parkinsonian animals
Slow Release Pellet Implantation
By onThis protocol describes how to subcutaneously implant slow-release pellets into mice.
Image Processing and 3D Reconstruction
By onThis workflow was used to analyze a Krios dataset of the PI3KC3-C1/RAB1A Complex and generate a reconstruction of three distinct conformational states of the VPS34 lipid kinase domain.
Unbiased MD simulations of POPI entry into VPS34KD
By onThis protocol details molecular dynamics simulations of the kinase domain of VPS34 in a membrane containing 15% of POPI lipids and analysis of POPI entry into the catalytic site.
Measuring lysosomal exocytosis by Flow cytometry
By onFlow cytometry can be used to measure lysosomal exocytosis by analyzing changes in fluorescence intensity of lysosomal markers in cells, providing a protocol for studying this cellular process.
Analysis of ER Flux in Cultured Induced Neurons using Keima ER reporters
By onAssociated with preprint: https://doi.org/10.1101/2023.06.26.546565
Analysis of ER structures in Cultured Induced Neuron axons
By onAssociated with preprint: https://doi.org/10.1101/2023.06.26.546565
Characterizing spatial and temporal properties of ER-phagy receptors
By onAssociated with preprint: https://doi.org/10.1101/2023.06.26.546565
Single cell/nuclei RNAseq analysis
By onThis protocol describes the process for the single cell/nuclei RNA sequencing data of the manuscript "L1retrotransposons drive human neuronal transcriptome complexity and functional diversification " from fetal forebrain and adult prefrontal cortex tissue.
CD8 Cell Density In Substantia Nigra And Cerebral Peduncle Image Analysi
By onQuPath is a bioimage analysis software designed for digital pathology and whole slide image analysis. This protocol describes how to measure CD8 density in the substantia nigra and cerebral peduncle using haematoxylin and DAB-stained brain sections.
Staining of cells with GolgiTracker for Golgi flow cytometry analysis
By onMethod that allows the staining of intact Golgi using GolgiTracker for subsequent flow cytometry analysis.
Pole Test
By onThe protocol describes the pole test for assessing motor coordination and balance in rodents.
Image processing to investigate NEMO recruitment and involvement in mitophagy and inflammatory signaling
By onExtensive image processing techniques were used to analyze cellular mechanisms, including deconvolution, machine learning, and manual identification of structures. Creative approaches were employed to ensure reliable and reproducible results.
