NeuroQP Docs

Exporting your project

Use the Export view when you want to download a reproducible snapshot of your project.

NeuroQP prepares the export as a single ZIP file that you can download once it is ready.

Export size

Exports can get large.

As a rough guide, around 4 GB for 100 slices is normal, depending on selected contents and image sizes.

What you can include

You can choose one or more export parts:

  • Data: processed images used for analysis, slice metadata, and cell detection masks where available
  • Registration: atlas metadata, registration points, slice coordinates, animal tilt, section geometry and sampled atlas region labels, plus detail alignment points for 4x reference + detail projects.
  • Classification: selected classifier metadata and evaluation metrics, current training-sample labels, per-slice classification result arrays, and available detection-overlap match results

Project metadata, including the project workflow and staining roles, is always included automatically.

For independent-detection projects, classification results can include marker-specific detections. For co-expression workflows, detection-overlap match results are included when they are available and current for the selected detections.

Registration geometry in the export

Registration exports record each positioned slice’s AP coordinate, animal tilt and section plane. They also include the sampled atlas region labels and the information needed to interpret their coordinates.

The label image identifies anatomical regions; it is not a microscopy image or a cell-detection mask.

A registration without a saved AP coordinate is exported without sampled atlas labels. Preparing registration exports may take longer because NeuroQP samples the atlas sections for the archive.

How export works

  1. Open the Export view.
  2. Select the parts you want to include.
  3. If you export classification, choose the classifier to use for each staining.
  4. Click Prepare Export.
  5. Wait until the ZIP file is ready, then download it.

The download is prepared in the background, so you do not need to keep the page open the whole time.

Open exported images in ImageJ

Exported images use BigTIFF, a TIFF variant that supports large files. To open them in ImageJ or Fiji, use Plugins → Bio-Formats → Bio-Formats Importer. Fiji includes Bio-Formats; standalone ImageJ requires installing the plugin. ImageJ’s built-in TIFF reader does not support BigTIFF and may show a generic error when opening these files.

Download a Statistics figure

To download a figure, use Export SVG on a Statistics dashboard plot or in its fullscreen viewer. This captures that plot's current displayed combination, including its panels and titles, as an editable vector figure.

A figure download and a project export serve different purposes. Use the ZIP export for project data and analysis metadata; use SVG for the visual comparison shown in Statistics.

See Using the statistics dashboard for figure downloads and viewing controls.

Analyze the export in Python

Install the optional NeuroQP Python package when you want to use the exported project in your own analysis:

python -m pip install neuroqp

The package opens the ZIP directly and keeps animals, slices, stainings, images, registrations, classifications, and cell matches linked. See Analyze an Export with Python for a minimal example and links to the complete Python documentation.