NeuroQP Docs

Data requirements

Before uploading, each slice should include the images required by the project's acquisition mode and image roles.

NeuroQP supports 10x and 20x analysis magnifications. Some projects also require a 4x anatomical reference.

4x reference + detail projects

Use this acquisition mode when each slice has a whole-slice reference image and separate detail images.

Shared cell detection

For each slice, prepare:

  • anatomical reference image at 4x
  • Cell Detection image at the project detail magnification
  • Classification images at the project detail magnification

Example with DAPI, cFos, and NeuN in a 10x project:

  • DAPI 4x as Anatomical reference
  • DAPI 10x as Cell Detection
  • cFos 10x as Classification
  • NeuN 10x as Classification

If NeuN, Hoechst, or another nuclear marker is the cell detection source, use that staining as Cell Detection instead of DAPI.

Independent marker detection

For each slice, prepare:

  • anatomical reference image at 4x
  • each Detection & Classification marker at the project detail magnification

Example with cFos and TRAP in a 20x project:

  • cFos 4x or another selected staining at 4x as Anatomical reference
  • cFos 20x as Detection & Classification
  • TRAP 20x as Detection & Classification

High-res whole-slice projects

Use this acquisition mode when the full brain slice is imaged directly at 10x or 20x.

For each slice, prepare images at the project detail magnification. No 4x image is required.

Example with cFos and TRAP in a 10x project:

  • cFos 10x as Anatomical reference and Detection & Classification
  • TRAP 10x as Detection & Classification

Because the anatomical reference is already high resolution, NeuroQP skips detail-to-reference FFT alignment.

Detail-only projects

Use this legacy acquisition mode when each uploaded image is already a 10x or 20x detail image and there is no whole-slice reference.

For each slice, prepare:

  • detail images at the project magnification
  • filenames or upload assignments that identify the animal, AP coordinate, staining, and intended brain region
  • the detail image pixel size in um/px

No 4x image is required. Atlas registration and Anatomical reference roles are not used. Each uploaded whole image is assigned directly to a selected brain region.

Supported formats

Upload supports standard microscopy image formats:

  • TIFF (.tif, .tiff)
  • PNG (.png)
  • JPEG (.jpg, .jpeg)

Imaging best practices

Use consistent acquisition settings across animals and conditions.

  • Keep exposure and gain consistent within a channel
  • Ensure sharp focus before batch acquisition
  • Avoid clipping saturated regions
  • Keep channel naming consistent with Study setup aliases
  • Verify magnification labels in exported filenames

Strong acquisition variability can reduce comparability across slices and groups.