Jun 23, 2024
  • 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
  • Eroglu_Lab
Icon indicating open access to content
QR code linking to this content
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 23, 2024
Last Modified: June 23, 2024
Collection  Integer ID: 102279
Keywords: quantification of synapse, using synbot, vivo synapse, paper synbot, synapse, synbot with manual, synbot protocols protocol, details of rat neuron, rat neuron, source image analysis software, astrocyte culture
Funders Acknowledgements:
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
Name
Installing FIJI and SynBot (Windows Version)
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
Installing FIJI and SynBot (Mac Version)
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
ilastik install and run for Syn Bot (Windows Version)
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
ilastik install and run for Syn Bot (Mac Version)
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
Quantifying Synaptic Colocalizations with SynBot (Manual Thresholding)
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
Quantifying Synaptic Colocalizations with SynBot (ilastik Thresholding)
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
Synapse Staining - IHC - VGluT1 and PSD95 - Mouse Brain Sections
Version 1
Created by
Image of Juan Ramirez
Juan Ramirez
Protocol
Name
Astrocyte Isolation and ACM Production
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
Glia-Free Cortical Neuronal Feeding Schedule - Synapse Formation
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
Glia-Free Cortical Neuron Culture
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
Synapse Quantification with Puncta Analyzer
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University
Protocol
Name
Creating Simulated Synapse Images
Version 1
Created by
Image of Justin T Savage, Duke University
Justin T SavageDuke University