Study setup overview
Study setup defines how NeuroQP interprets uploaded files and how project data is summarized later.
It controls:
- which stainings are expected
- which role each staining plays in analysis
- which animals, groups, conditions, and sex metadata are tracked
- which atlas and brain regions are used in analysis
- whether selected brain regions are treated as joint measurements or separated into left and right hemisphere measurements
Atlas and brain regions
The selected atlas defines the brain regions available for the project.
Most projects use a brain atlas, such as the Allen Mouse Brain Atlas, Kim Unified Mouse Brain Atlas, or Waxholm Sprague Dawley Rat Brain Atlas. Mouse spinal cord projects can use the Allen Mouse Spinal Cord Atlas instead.
Atlases do not all support the same regions. For example, the Kim Unified Mouse Brain Atlas has more mouse brain subregions than the Allen Mouse Brain Atlas, while the Allen Mouse Spinal Cord Atlas provides spinal cord regions instead of brain regions.
Hemisphere mode
Hemisphere mode controls whether selected brain regions are analyzed as one combined measurement or separated into left and right measurements.
Use Joint when each selected brain region should be treated as one combined measurement.
Use Separate when you want NeuroQP to track left and right hemisphere measurements separately. In Separate mode, you can still mark individual selected brain regions as joint if hemisphere splitting is not useful for that region.
Recommended order
To avoid rework, configure Study setup in this order:
- Review stainings and roles
- Configure Experiment Setup
- Define groups and conditions if enabled
- Add animals
- Select brain regions
Project checklist
For registered projects, make sure you have one Anatomical reference role.
For Detail only projects, do not assign an Anatomical reference role. Each slice must instead be assigned to a selected brain region.
For shared cell detection, make sure you have:
- one Cell Detection role
- any Classification roles you want to quantify
- at least one animal
- at least one brain region
For independent marker detection, make sure at least one staining has the Detection & Classification role.
If groups are enabled, at least one group is required. If conditions are enabled, at least two conditions are required.
Use the Study validation panel as a guide for what to configure next.
You can update much of Study setup later. If you change setup after uploading data, review assignments and processing status to keep the project consistent.