Jun 23, 2024

Public workspaceSynBot Protocols V.2

  • 1Department of Neurobiology, Duke University Medical Center, Durham, NC 27710;
  • 2Department of Cell Biology, Duke University Medical Center, Durham, NC 27710;
  • 3Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710
Open access
Collection CitationJustin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu 2024. SynBot Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl4qewjvo5/v2Version created by Justin T Savage
License: This is an open access collection distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this collection and it's working
Created: June 09, 2023
Last Modified: June 23, 2024
Collection Integer ID: 102279
Funders Acknowledgement:
NIH ROI
Grant ID: AG059409
NIH ROI
Grant ID: NS102237
BRAIN Initiative
Grant ID: U19NS123719
Chan Zuckerberg Initiative, Neurodegeneration Challenge Network
Grant ID: 2018-191999
Chan Zuckerberg Initiative, Neurodegeneration Challenge Network
Grant ID: DAF2021-237435
Michale J Fox Foundation
Grant ID: ASAP-020607
NINDS
Grant ID: F31NS125985
Howard Hughes Medical Institute
Pew Latin American Fellows Program in the Biomedical Sciences
Foerster-Bernstein Post-Doctoral Fellowship Program for Women in STEM
Holland-Trice Scholars Award for high risk/high impact discovery in research in Basic Brain Science and Brain Diseases
Aligning Science Across Parkinson’s
Grant ID: ASAP-020607
Abstract
Protocols related to the paper SynBot: An open-source image analysis software for automated quantification of synapses. Includes details of rat neuron and astrocyte culture, in vitro synapse staining, in vivo synapse staining, and using SynBot with manual or ilastik thresholding.
Files
Protocol
Installing FIJI and SynBot (Windows Version)
Name
Installing FIJI and SynBot (Windows Version)
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
Installing FIJI and SynBot (Mac Version)
Name
Installing FIJI and SynBot (Mac Version)
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
ilastik install and run for Syn Bot (Windows Version)
Name
ilastik install and run for Syn Bot (Windows Version)
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
ilastik install and run for Syn Bot (Mac Version)
Name
ilastik install and run for Syn Bot (Mac Version)
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
Quantifying Synaptic Colocalizations with SynBot (Manual Thresholding)
Name
Quantifying Synaptic Colocalizations with SynBot (Manual Thresholding)
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
Quantifying Synaptic Colocalizations with SynBot (ilastik Thresholding)
Name
Quantifying Synaptic Colocalizations with SynBot (ilastik Thresholding)
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
Synapse Staining - IHC - VGluT1 and PSD95 - Mouse Brain Sections
Name
ForkSynapse Staining - IHC - VGluT1 and PSD95 - Mouse Brain Sections
Version 1
Juan Ramirez
Juan Ramirez
Protocol
Astrocyte Isolation and ACM Production
Name
Astrocyte Isolation and ACM Production
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
Glia-Free Cortical Neuronal Feeding Schedule - Synapse Formation
Name
Glia-Free Cortical Neuronal Feeding Schedule - Synapse Formation
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
Glia-Free Cortical Neuron Culture
Name
Glia-Free Cortical Neuron Culture
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
Synapse Quantification with Puncta Analyzer
Name
Synapse Quantification with Puncta Analyzer
Version 1
Justin T Savage
Justin T SavageDuke University
Protocol
Creating Simulated Synapse Images
Name
Creating Simulated Synapse Images
Version 1
Justin T Savage
Justin T SavageDuke University