What happens after upload

After files are uploaded, NeuroQP runs processing jobs automatically in the background when the required images are available.

The exact pipeline depends on acquisition mode and image roles.

Atlas registration

Atlas registration runs on the project's Anatomical reference image.

In 4x reference + detail projects, this is usually a 4x image.

In high-res whole-slice projects, this is a 10x or 20x full-slice image.

Atlas registration places the slice in atlas space, estimates AP position, and creates the point mapping used for region assignment.

Detail-only projects skip atlas registration. NeuroQP uses the assigned brain region on each slice instead of computing region membership from atlas boundaries.

Detail-to-reference alignment

This step runs only for 4x reference + detail projects.

It places 10x or 20x detail images onto the anatomical reference image.

High-res whole-slice projects skip this step because the analyzed image is already the anatomical reference.

Detail-only projects also skip this step because there is no whole-slice reference image.

Cell Detection processing

For shared cell detection projects, NeuroQP runs cell detection on the Cell Detection staining.

This produces the shared cell or nuclei population used by Classification roles.

Detection & Classification processing

For independent marker detection projects, NeuroQP runs detection separately for each Detection & Classification staining.

Each marker gets its own detection output, cell metadata, training samples, classifier, Results, and Statistics path.

Classification and statistics

Classifier training starts only when you explicitly train a model.

Statistics are calculated from selected classifier outputs after Results are available. For independent marker detection projects, only accepted marker-positive cells are counted in downstream summaries.

Timing expectations

Processing duration depends on image size, queue load, and project volume.

You can continue working in the app while processing runs. Refreshing the Data view shows current status updates. If processing fails, use retry controls where available.