Quantitative Neuroanatomy Course

Part of the I2K 2020 conference.

Summary

The course is organized in 3 parts:

Part 1: Tracing

​ Overview, GUI-based controls and basic scripting

Part 2: Visualization

​ Neuroanatomy viewers and their scripting capabilities

Part 3: Analysis

​ Single-cell morphometry, databases and brain atlases, and quantitative analyses of cell groups

Requirements

SNT is available in Fiji and is currently distributed through the NeuroAnatomy update site.

1. Download and Install Fiji.
2. Subscribe to NeuroAnatomy update site:
   1. the Run the Fiji Updater (Help › Update..., the penultimate entry in the Help › menu)
   2. Click Manage update sites
   3. Select the Neuroanatomy checkbox
   4. Click Apply changes and Restart Fiji. SNT commands are registered under Plugins>Neuroanatomy> in the main menu and SNT scripts under Templates>Neuroanatomy> in Fiji's Script Editor.
3. For Jupyter notebooks, you will need to install pyimagej by following these instructions

NB:

• We recommend to re-run the updater on the day of the course to ensure you can access the most recent versions of the demos scripts
• It is perfectly fine to keep multiple Fiji installations in your system
• Due to lack of time, we are not going to cover sciview integration, so you don't need to subscribe to the sciview update site
• If you are using a laptop, an external mouse may be useful during part 1

Resources

SNT Manuscript | SNT Manuscript scripts | User Documentation | Forum | Source Code | API