Jun 13, 2024

Public workspaceInstalling FIJI and SynBot (Mac Version)

DOI
dx.doi.org/10.17504/protocols.io.14egn6936l5d/v1
  • 1Department of Neurobiology, Duke University Medical Center, Durham, NC 27710
Justin T Savage
Open access
DOI: dx.doi.org/10.17504/protocols.io.14egn6936l5d/v1
Protocol Citation: Justin T Savage 2024. Installing FIJI and SynBot (Mac Version). protocols.io https://dx.doi.org/10.17504/protocols.io.14egn6936l5d/v1
License: This is an open access protocol 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 protocol and it's working
Created: June 10, 2024
Last Modified: June 13, 2024
Protocol Integer ID: 101527
Abstract
Video instructions for installing FIJI and the software needed for SynBot on MacOS.

Video

Install FIJI
Install FIJI
0:00-0:30 Download FIJI from https://fiji.sc .
0:30-1:11 Give Mac permission to open FIJI since it is from an outside developer.
Install SynBot
Install SynBot
1:11-1:56 Download code from the SynBot GitHub repository https://github.com/Eroglu-Lab/Syn_Bot .

1:56-2:39 Move SynBot java plugins (JAR files) to the FIJI plugins folder. The ilastik4ij_Syn_Bot-1.8.2-SNAPSHOT.jar and SynQuantExtra-1.2.9.jar files are required for running SynBot.

Run SynBot
Run SynBot
2:39-3:00 Launch FIJI and open SynBot by dragging the SynBot.ijm file into FIJI.
3:00-3:11 Prepare your image folder. Create a folder for your experiment with subfolders for experimental groups. Each experimental group folder should contain only image files. Multiple experimental groups are not required, but your files must follow the Experiment/Group/Image structure.
3:11-4:53 Run SynBot (see the SynBot manual thresholding protocol for more information).
4:53-5:04 View results in Summary.csv file.