NeuroQP Docs

Stainings

Stainings define the imaging channels you expect in your study and the role each channel plays in processing.

The same staining name can mean different things in different projects. For example, DAPI might be the anatomical reference and Cell Detection staining in one project, while NeuN or another nuclear marker might fill that role in another project.

What to configure

For each staining, define:

  • Name: Main channel label used in your project
  • Aliases: Alternate labels that may appear in filenames
  • Color: Visual aid for image display and overlays
  • Comments: Optional internal notes
  • Roles: How NeuroQP should use this staining

Common roles

Anatomical reference

The image used for atlas registration.

In 4x reference + detail projects, this is usually a 4x whole-slice image. In high-res whole-slice projects, this is a 10x or 20x full-brain image.

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

Cell Detection

The image used to detect a shared population of cells or nuclei.

DAPI is a common example, but this role can also be used for another nuclear or cell-source marker such as Hoechst or NeuN when that is the appropriate detection source.

Classification

A marker image classified against cells detected from the Cell Detection staining.

Use this when you want ON/OFF expression calls for cells from a shared detection source.

Detection & Classification

A marker image where cells or marker-positive objects are detected directly from that staining, then classified to accept or reject candidates.

Use this when you don't have a nuclear stain and each marker staining should define its own marker-positive cells independently.

Locked roles

Some roles define project behavior and may be locked after project creation. If you need to change a project-defining role after uploading data, create a new project or coordinate carefully before continuing analysis.

Recommendations

  • Use stable, short staining names
  • Add aliases that match real microscope export labels
  • Keep naming consistent across contributors
  • Review roles before uploading large batches

Warning

If you remove a staining later, linked uploaded image assignments for that staining may be cleared and need reassignment.