Jun 24, 2024

Public workspaceSynBot Protocols V.2

Cell Reports Methods
DOI
dx.doi.org/10.17504/protocols.io.3byl4qewjvo5/v2
  • 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
Justin T Savage
Icon indicating open access to content
QR code linking to this content
DOI: dx.doi.org/10.17504/protocols.io.3byl4qewjvo5/v2
Collection Citation: Justin 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 24, 2024
Collection Integer ID: 102279
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
Icon representing the file Installing FIJI and SynBot (Windows Version)
Name
Installing FIJI and SynBot (Windows Version)
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file Installing FIJI and SynBot (Mac Version)
Name
Installing FIJI and SynBot (Mac Version)
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file ilastik install and run for Syn Bot (Windows Version)
Name
ilastik install and run for Syn Bot (Windows Version)
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file ilastik install and run for Syn Bot (Mac Version)
Name
ilastik install and run for Syn Bot (Mac Version)
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file Quantifying Synaptic Colocalizations with SynBot (Manual Thresholding)
Name
Quantifying Synaptic Colocalizations with SynBot (Manual Thresholding)
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file Quantifying Synaptic Colocalizations with SynBot (ilastik Thresholding)
Name
Quantifying Synaptic Colocalizations with SynBot (ilastik Thresholding)
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file Synapse Staining - IHC - VGluT1 and PSD95 - Mouse Brain Sections
Name
ForkSynapse Staining - IHC - VGluT1 and PSD95 - Mouse Brain Sections
Version 1
,
Juan Ramirez
Protocol
Icon representing the file Astrocyte Isolation and ACM Production
Name
Astrocyte Isolation and ACM Production
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file Glia-Free Cortical Neuronal Feeding Schedule - Synapse Formation
Name
Glia-Free Cortical Neuronal Feeding Schedule - Synapse Formation
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file Glia-Free Cortical Neuron Culture
Name
Glia-Free Cortical Neuron Culture
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file Synapse Quantification with Puncta Analyzer
Name
Synapse Quantification with Puncta Analyzer
Version 1
, Duke University
Justin T SavageDuke University
Protocol
Icon representing the file Creating Simulated Synapse Images
Name
Creating Simulated Synapse Images
Version 1
, Duke University
Justin T SavageDuke University