Brain regions

Brain regions define which anatomical areas are included in your study outputs and statistics. They are also shown in the atlas registration and might be helpful for fine atlas adjustments

Selected regions determine where quantification results are aggregated and reported.

The brain region selection has two sides: On the left side you have all regions of the brain, and on the right side you have the regions that are selected for your study. You cann add a brain region by clicking the + button on a region in the left panel, and remove it by clicking the X button inthe right panel.

Finding your brain regions

You can also search search for regions by name using the search bar. It will filter the complete list and only show the brain regions matching your search.

You can also preview the actual brain region in the atlas if you click the Preview. This will show a viewer and give you a quick overview of the brain region you select.

Setup guidance

• Select only regions relevant to your study question
• Regions should be fully inside the 20x images you upload in the data
• Keep selection focused to improve interpretability

At least one brain region is required for a valid study setup.

Recommendations

• Start with your primary target regions
• Decide on the level of detail that you want in your final statistics and pick the brain regions accordingly
• You can modify region at any time without any issues, so you don't have to completely define all the regions that might be interesting for your study when just starting out.
• Come back to changing brain regions once you have some data uploaded and start looking at statistics.