Release Notes

Statistics now supports a saved dashboard shared with your project team. Add, arrange and resize plots, and configure each plot’s stainings, metrics, filters and appearance.

Your team can keep useful comparisons and save plot settings for publication figures. The layout and settings persist between visits and when project data changes, so updated results can be viewed with the same configuration.

You can now adjust the atlas orientation to match roughly coronal mouse and rat brain sections.

• Adjust position and tilt together. Open the AP coordinate control to adjust left/right and dorsal/ventral tilt, with live previews in both viewers.
• Apply tilt across an animal. All slices assigned to that animal share the orientation while keeping their individual AP coordinates and registration points.
• Use the saved orientation throughout your analysis. Training and Results overlays, regional counts and areas, and anatomical cell and density plots now account for tilted sections.
• Export the section geometry. Registration exports include tilt settings and sampled atlas region labels.

After changing animal tilt, review the affected registrations and run Process results to refresh measurements. Tilt is adjusted manually; automatic tilt estimation and sagittal or horizontal sections are not supported.

See the atlas examples and registration workflow in When a coronal brain section is not quite coronal.

NeuroQP’s new Region-free Statistics make it easy to see where spatial patterns appear across the brain, without first deciding which brain regions to analyze. Cell and density views reveal distributions directly in atlas space, making unexpected hotspots, shifts, and group differences easier to spot.

This qualitative overview supports experimentation and discovery: explore the complete spatial pattern first, then develop quantitative analyses based on what the data reveals—not only on regions chosen in advance.

NeuroQP now makes it easier to review and analyze projects from your phone or tablet.

• Browse projects and study details
• Inspect images, registrations, and training samples
• Select existing classifier models and run analyses
• Explore results in the viewer or table
• Configure and view statistics plots in fullscreen

Creating or editing projects, uploading data, editing registrations or training samples, training models, and exporting files still require desktop.

Projects can now have an owner, making it easier to see who in your lab is working on what. Use My projects or filter by a lab member to quickly find the projects you need. Projects assigned to former members remain easy to find and reassign.

Project ownership is for organizing work within your lab only. It does not change access—everyone in your organization can still open every project.

You can now add multiple animals to a project at once from an Excel or CSV spreadsheet. Match your columns, review the animals, and import their groups, conditions, sex, and comments in one step.

NeuroQP Python 0.1.0 is now available. Install it with pip install neuroqp to open a NeuroQP project export, navigate animals, slices, stainings, images, and atlas registrations, and load classification and cell-match results as NumPy arrays for custom analysis.

Read the NeuroQP Python documentation or view the package on PyPI.

NeuroQP now supports the Allen Mouse Spinal Cord Atlas for mouse spinal cord workflows. This beta release adds the atlas as a selectable option for projects, alongside the existing brain atlases.

Please treat spinal cord atlas results as beta while we continue validating registration, region overlays, and downstream statistics.

NeuroQP now supports anatomical labels for atlas slice positions.

For spinal cord projects, upload filenames and atlas slice pickers can use labels such as C1, T9, or L3 instead of exact coordinates.

NeuroQP now supports left/right hemisphere measurements in Results and Statistics.

When Hemisphere mode is Separate, supported brain regions can appear as separate left and right measurements in tables, viewers, and plots.

Regions kept joint remain combined, so you can split only the regions where hemisphere-level analysis is useful.

NeuroQP now supports the Waxholm Sprague Dawley Rat Brain Atlas for rat brain workflows. This beta release adds the atlas as a selectable option for projects, alongside the existing mouse brain atlases.

Please treat Waxholm rat atlas results as beta while we continue validating registration, region overlays, and downstream statistics.

Improved the image registration viewer for a smoother, more responsive experience when aligning brain slice images with atlas regions.

This update modernizes the viewer foundation, improves overlay rendering, and prepares registration workflows for higher-resolution image navigation.

NeuroQP now gives you more control over classifier models for each staining.

You can import pre-trained models or models from another project, rename and describe models, and delete models that are no longer needed.

If you are part of multiple labs, organization switching is now available under Manage organization from your avatar menu.

NeuroQP now has a more consistent interface across Study, Registration, Training, and Results.

This update improves layouts, viewer controls, table controls, brain-region selection, and Results co-expression review so the main workflow feels more unified across the app.

NeuroQP now supports the Kim Unified Mouse Brain Atlas in addition to the Allen Mouse Brain Atlas! The Kim atlas includes more detailed mouse brain subregions.

You can change the used atlas in the Study tab where you select your brain regions.

NeuroQP now supports legacy Detail only projects without a whole-slice reference image.

You can upload 10x or 20x detail images, assign them directly to brain regions, and provide pixel size for area-based measurements.

When a whole-slice reference is available, we still recommend using a registered project mode.

Statistics now has more plot options and better controls for publication-ready figures.

• New plot types: bars, vertical bars, dot/strip, box/violin, effect size, and scatter plots
• Manual ranges for heatmaps, anatomical plots, bar-style plots, and mirrored plot axes
• Shared-range controls for comparing plots on the same scale
• Selectable first color for grouped plot palettes
• Improved heatmap, mirrored, and anatomical plot layouts, legends, and SVG exports

Fix: Training, cell detection, and atlas registration now update queued, processing, and error states more quickly.

Registration, Training, and Results viewers now include compact brightness controls for adjusting image display.

NeuroQP now supports more flexible staining workflows beyond the original DAPI-centered setup.

• Project creation now allows you to specify different project configurations
• Cell detection can use a normal cell nuclei marker such as DAPI or NeuN in cell-counting projects
• Marker stainings such as cFos or TRAP can run independent cell detection when there is no shared DAPI/NeuN nuclei staining for cell counting
• Full-brain high-resolution slice projects are supported at 10x and 20x without a separate 4x anatomical reference image
• Full-brain high-resolution projects skip detail-to-reference alignment because the analyzed image is already the anatomical reference
• Training, Results, Statistics, and co-expression now understand independent-detection projects and their marker-positive cell semantics

Existing 4x reference plus 10x or 20x detail projects continue to work as before.

NeuroQP now supports projects built around 10x detail images in addition to 20x.

With this release:

• You choose the detail magnification when creating a project
• Upload validation now supports 4x, 10x, and 20x image labels
• Alignment, cell detection, and downstream analysis follow the project's selected detail magnification
• Existing 20x projects continue to work as before

You can now export a project as a single reproducible archive. This is part of our ongoing effort to make your experiments reproducible and support you with writing your own code on top of NeuroQP.

This export can include:

• Original uploaded images
• Registration point pairs and AP values
• 4x detail alignment points
• Cell detection masks
• Training samples
• One selected classifier per staining

• Automated 20x DAPI cell detection
• Whole-slice brain atlas registration from 4x DAPI images
• 20x overlay placement and manual registration refinement
• Custom cell-classifier training for staining-specific analysis
• Results review in tables and image viewers
• Brain-region statistics and publication-ready plot exports
• Co-expression analysis in the statistics workflow
• Public docs covering project setup, uploads, registration, training, results, and statistics