What happens after upload

After files are uploaded, Neuro QP runs processing jobs automatically in the background.

Automatic processing pipeline

1. 20x-to-4x DAPI alignment

Runs when both DAPI 20x and DAPI 4x images are available for a slice.

This step places the 20x high-resolution data to the low-resolution 4x full brain slice reference.

You will see a gray spinning icon while it is running. If it completes successfully, it will appear as a green icon linking DAPI 20x to the DAPI 4x image

2. Atlas registration

Runs when DAPI 4x is available.

This places the slice in atlas space and determines AP position and point mappings. The atlas registration tries to detect the AP coordinate automatically and checks if it differs greatly from the already specified AP coordinate you have defined during the upload. It will not overwrite the AP coordinate, but warn you if it things that the AP coord was specified wrongly.

While it is running, it will appear as a gray spinning icon. Once it finishes successfully, you will see a green Atlas registration indicator on the slice.

3. Cell detection

Runs when DAPI 20x is available.

This detects cells and produces per-slice cell counts used in downstream statistics.

It will appear as a gray spinning icon during processing. Once finished, it will show the cell counts in green.

Timing expectations

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

• Small batches: Usually complete quickly
• Large batches: Can take longer while jobs are queued and processed asynchronously

You can continue working in the app while processing runs. Refreshing the Data view will show current status updates. If any processing fails, it will show up as failed and you can retry it manually.