Jun 13, 2024
Installing FIJI and SynBot (Mac Version)
- Justin T Savage1
- 1Department of Neurobiology, Duke University Medical Center, Durham, NC 27710
- Eroglu_Lab
External link: https://doi.org/10.1016/j.crmeth.2024.100861
Protocol Citation: Justin T Savage 2024. Installing FIJI and SynBot (Mac Version). protocols.io https://dx.doi.org/10.17504/protocols.io.14egn6936l5d/v1
Manuscript citation:
Savage JT, Ramirez JJ, Risher WC, Wang Y, Irala D, Eroglu C (2024) SynBot is an open-source image analysis software for automated quantification of synapses. Cell Reports Methods 4(9). doi: 10.1016/j.crmeth.2024.100861
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
Keywords: synbot on maco, installing fiji, synbot, maco, video instruction, mac version, software
Abstract
Video instructions for installing FIJI and the software needed for SynBot on MacOS.
Troubleshooting
Install FIJI
0:30-1:11 Give Mac permission to open FIJI since it is from an outside developer.
Install SynBot
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
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.
4:53-5:04 View results in Summary.csv file.