Part of the I2K 2020 conference.
| Sessions | |
|---|---|
| 1 | 2020-11-30 14:00 – 2020-11-30 18:00 UTC |
| 2 | 2020-12-01 22:00 – 2020-12-02 02:00 UTC |
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
SNT is available in Fiji and is currently distributed through the NeuroAnatomy update site.
- Download and Install Fiji.
- Subscribe to NeuroAnatomy update site:
- the Run the Fiji Updater (Help › Update..., the penultimate entry in the Help › menu)
- Click Manage update sites
- Select the Neuroanatomy checkbox
- 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.
- 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
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