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

Atlas and brain regions

Atlases are interchangeable within the same animal and anatomical target, such as mouse brain, but they do not all support the same regions. The Kim Unified Mouse Brain Atlas has more subregions than the Allen Mouse Brain Atlas, and some Kim regions are not available in Allen.

Recommended order

To avoid rework, configure Study setup in this order:

1. Review stainings and roles
2. Configure Experiment Setup
3. Define groups and conditions if enabled
4. Add animals
5. 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.