Presets and Image Roles

Presets fill in a starting set of stainings and image roles during project creation.

A preset is only a starting point. The lasting behavior of the project comes from the acquisition mode, the nuclear marker setting, and the roles assigned in the Stainings and roles table.

Shared cell detection

Use this preset when one nuclear or cell-source staining defines the cells and other marker stainings classify those cells.

Typical setup:

• DAPI, Hoechst, or NeuN: Anatomical reference and Cell Detection, when registration is used
• cFos, TRAP, or another marker: Classification

This setup supports total cells, marker-positive cells, marker-negative cells, % ON, and density metrics.

Independent marker detection

Use this preset when you don't have a nuclear stain. Each marker staining detects and classifies its own marker-positive cells independently.

Typical setup:

• cFos: Anatomical reference and Detection & Classification, when registration is used
• TRAP: Detection & Classification

Each marker has its own detection and classifier path.

Detail-only projects

Detail-only projects do not use an Anatomical reference role.

Use Detail only only for legacy datasets where no whole-slice reference image is available. Each uploaded whole image is assigned directly to a selected brain region, so this mode does not provide the benefits of atlas registration.

Role reference

• Anatomical reference: used for atlas registration. Not available in Detail only projects.
• Cell Detection: used to detect a shared cell or nuclei population.
• Classification: classified against cells from the Cell Detection staining.
• Detection & Classification: detects marker-positive candidates directly on that staining, then uses classification to accept or reject them.

Editing roles

Review roles before uploading data.

Some project-defining roles may be locked after project creation because changing them would invalidate downstream processing assumptions.